WO2018195951A1

WO2018195951A1 - Integrated sample collection, processing and analysis systems

Info

Publication number: WO2018195951A1
Application number: PCT/CN2017/082492
Authority: WO
Inventors: Xiang Li
Original assignee: Coyote Diagnostics Lab (beijing) Co Ltd
Current assignee: Coyote Diagnostics Lab (beijing) Co Ltd
Priority date: 2017-04-28
Filing date: 2017-04-28
Publication date: 2018-11-01
Anticipated expiration: 2019-10-28

Abstract

Systems, electronic devices(101, 201, 401, 501), and methods for collecting, processing, and/or analyzing samples(214, 1509, 1609) from a subject in a format of an integrated sample collection, processing and analyzing system, so as to make sample analysis more accessible to users.

Description

INTEGRATED SAMPLE COLLECTION, PROCESSING AND ANALYSIS SYSTEMS

BACKGROUND

Molecular diagnostic methods and kits enjoy wider and wider applications globally. Certain molecular diagnostic tools, such as nucleic acid amplification and sequencing, allow diagnosis and/or determination of health condition of a subject in a rapid and on-site manner, with minimal requirements for sample.

However, currently these molecular diagnostic methods and kits are only available to potential users via a medical facility or pharmacy. This significantly reduces the accessibility of these molecular diagnostic tools to potential users, and reduces the compliance of the users. Therefore, there remains a need in the art to more efficiently dispense these molecular diagnostic tools to potential users.

SUMMARY

The present disclosure provides systems, electronic devices, and methods for collecting, processing, and/or analyzing samples from a subject. By using an integrated sample collection, processing and analyzing system, sample analysis assays are readily accessible to users.

In one aspect, the present disclosure involves a system for collecting and/or processing a biological sample of a subject, comprising:

a communication interface in communication with an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in the biological sample of the subject； and

a dispensing unit comprising one or more computer processors operatively coupled to the communication interface, wherein the one or more computer processors are individually or collectively programmed to (a) receive the selection inputted by the user in the display of the electronic device, and (b) direct dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the one or more graphical elements include a plurality of graphical elements, each of which plurality of graphical elements corresponds to a given target assay among the plurality of target assays.

In some embodiments, the system comprises a sample processing unit that (1) receives the biological sample collected of the subject, and (2) processes the biological sample based on the at least one target assay to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In some embodiments, the sample collection unit and/or one or more reagents are included in a kit. In some embodiments, the kit includes a finger prick. In some embodiments, the kit includes a swap.

In some embodiments, the dispensing unit includes a plurality of kits including the kit, each of which plurality of kits is directed to a given target assay among the plurality of target assays.

In some embodiments, the kit is among a plurality of kits, and wherein the one or more computer processors are individually or collectively programmed to (1) monitor a quantity of the plurality of kits or a subset thereof, and (2) provide a notification when the quantity approaches or is below a threshold.

In some embodiments, the notification is directed over a network to a computer server that receives the notification.

In some embodiments, the dispensing unit includes an opening to permit dispensing of the kit based on the selection.

In some embodiments, the kit further comprises instructions for collecting the biological sample from the subject.

In some embodiments, the at least one target assay includes array hybridization, nucleic acid sequencing or nucleic acid amplification.

In some embodiments, the dispensing unit is directly coupled to the electronic device.

In some embodiments, the dispensing unit is remotely coupled to the electronic device.

In some embodiments, the dispensing unit is operatively coupled to the electronic device over a network.

In some embodiments, the user interface displays instructions for collecting the biological sample from the subject.

In some embodiments, the sample collection unit includes identifying information of the subject.

In some embodiments, the identifying information is anonymous.

In some embodiments, the identifying information is on a barcode.

In some embodiments, the identifying information is in a radio-frequency identification (RFID) tag.

In some embodiments, the user is the subject.

In some embodiments, the user is a healthcare provider of the subject.

In some embodiments, the one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for the at least one target analyte.

In some embodiments, the one or more reagents include a reverse transcriptase and a deoxyribonucleic acid (DNA) polymerase.

In some embodiments, the one or more reagents include reagents necessary for preserving the biological sample.

In some embodiments, the biological sample includes a soil or food sample.

In some embodiments, the food sample is a dairy sample.

In some embodiments, the dairy sample includes milk.

In some embodiments, the biological sample is a tissue or fluid of a subject.

In some embodiments, the tissue or fluid is stool.

In some embodiments, the biological sample is an oral or rectal swab.

In some embodiments, the one or more graphical elements permit the user to input a selection of one or more of a tissue type of the biological sample and disease.

In some embodiments, the disease is selected from a plurality of diseases.

In some embodiments, the disease is cancer.

In some embodiments, the at least one target analyte is associated with a disease.

In some embodiments, the disease is associated with a virus.

In some embodiments, the virus is an RNA virus.

In some embodiments, the virus is a DNA virus.

In some embodiments, the virus is selected from the group consisting of human immunodeficiency virus I (HIV I) , human immunodeficiency virus II (HIV II) , an orthomyxovirus, Ebola virus, Dengue virus, influenza viruses, hepevirus, hepatitis A virus, hepatitis B virus, hepatitis C virus, hepatitis D virus, hepatitis E virus, hepatitis G virus, Epstein-Barr virus, mononucleosis virus, cytomegalovirus, SARS virus, West Nile Fever virus, polio virus, measles virus, herpes simplex virus, smallpox virus, adenovirus, Coxsackie virus, and Varicella virus.

In some embodiments, the influenza virus is selected from the group consisting of H1N1 virus, H3N2 virus, H7N9 virus and H5N1 virus.

In some embodiments, the adenovirus is adenovirus type 55 (ADV55) or adenovirus type 7 (ADV7) .

In some embodiments, the hepatitis C virus is armored RNA-hepatitis C virus (RNA-HCV) .

In some embodiments, the Coxsackie virus is Coxsackie virus A16.

In some embodiments, the disease is associated with a pathogenic bacterium or a pathogenic protozoan.

In some embodiments, the pathogenic bacterium is a gram-positive or gram-negative pathogenic bacterium.

In some embodiments, the pathogenic bacterium is selected from the group consisting of Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Enterobacter sakazakii, Vibrio Parahemolyticus, and Shigella spp.

In some embodiments, the pathogenic bacterium is Mycobacterium tuberculosis.

In some embodiments, the pathogenic protozoan is Plasmodium.

In some embodiments, the pathogenic bacterium is Salmonella.

In some embodiments, the at least one target assay is an amplification protocol.

In some embodiments, the plurality of target assays are directed to different target analytes.

In some embodiments, the plurality of target assays are the same type of assay.

In some embodiments, the amount is a relative amount.

In some embodiments, the system has a footprint less than or equal to 100 feet².

In some embodiments, the footprint is less than or equal to 25 feet².

In some embodiments, the footprint is less than or equal to 9 feet².

In some embodiments, the dispensing unit has a footprint less than or equal to 100 feet².

In some embodiments, the footprint is less than or equal to 25 feet².

In some embodiments, the footprint is less than or equal to 9 feet².

In some embodiments, the dispensing unit is within 5 feet of the electronic device.

In some embodiments, the dispensing unit is within 1 foot of the electronic device.

In some embodiments, the dispensing unit is attached to the electronic device.

In some embodiments, the sample collection unit is selected based on a type of the biological sample.

In some embodiments, the electronic device is a mobile electronic device of the user or the subject.

In some embodiments, the dispensing unit is operatively coupled to the electronic device through the communication interface.

In some embodiments, the communication interface is in communication with the electronic device over a network.

In some embodiments, the communication interface is in communication with the electronic device through at least one electronic bus.

In some embodiments, the electronic device further includes a sensing unit that captures a characteristic of the subject.

In some embodiments, the one or more computer processors are individually or collectively programmed to receive the selection inputted by the user subsequent to the user being provided the characteristic.

In some embodiments, the characteristic is a sound, image or video having the subject.

In some embodiments, the characteristic is a temperature, resistance, impedance, capacitance of the subject.

In some embodiments, the communication interface is in communication with an authentication unit that authenticates the user.

In some embodiments, the authentication unit is a fingerprint scanner, retina scanner, or impedance scanner.

In some embodiments, the authentication unit is part of the electronic device.

In some embodiments, the authentication unit is part of the system.

In another aspect, the present disclosure involves an electronic device for processing a biological sample of a subject, comprising:

a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in a biological sample of a subject； and

one or more computer processors operatively coupled to the display screen, wherein the one or more computer processors are individually or collectively programmed to (a) receive the selection inputted by the user in the user interface, and (b) transmit the selection to a dispensing unit that directs dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the one or more graphical elements are part of a questionnaire displayed on the user interface, which questionnaire (i) provides one or more questions to the user and (ii) generates an output based on one or more responses of the user to the one or more questions, which output corresponds to the at least one target assay from the plurality of target assays

In some embodiments, the questionnaire is a guided questionnaire.

In some embodiments, the user is the subject.

In some embodiments, the user is a healthcare provider of the subject.

In some embodiments, the display screen is a capacitive touch screen or resistive touch screen.

In some embodiments, the electronic device further comprises a communication interface that brings the one or more computer processors in communication with the dispensing unit.

In some embodiments, the electronic device further comprises a sensing unit that captures a characteristic of the subject.

In some embodiments, the one or more computer processors are individually or collectively programmed to receive the selection inputted by the user subsequent to the user being provided the characteristic of the subject.

In some embodiments, the one or more computer processors are in communication with an authentication unit that authenticates the user.

In some embodiments, the authentication unit is part of the electronic device.

In another aspect, the present disclosure involves a system for processing a biological sample of a subject, comprising:

a communication interface in communication with (i) an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining a presence, absence or amount of at least one target analyte in the biological sample of the subject, and (ii) a dispensing unit that dispenses a kit based on the selection, wherein the kit comprises (1) a sample collection unit for collecting the biological sample of the subject, and (2) one or more reagents necessary for processing the biological sample of the subject based on the selection； and

a sample processing unit operatively coupled to the communication interface, wherein the sample processing unit (a) receives the biological sample of the subject, and (b) processes the biological sample based on the selection inputted by the user corresponding to the at least one target assay from the plurality of target assays, to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In some embodiments, the sample processing unit comprises an actuator that transfers the biological sample to or from one or more sample processing stations of the sample processing unit.

In some embodiments, the actuator is a robotic arm.

In some embodiments, the sample processing unit receives the biological sample in a sample collection unit.

In some embodiments, the sample collection unit includes a cap.

In some embodiments, the identifying information is anonymous.

In some embodiments, the identifying information is on a barcode.

In some embodiments, the sample processing unit is directly coupled to the electronic device.

In some embodiments, the sample processing unit is remotely coupled to the electronic device.

In some embodiments, the sample processing unit is operatively coupled to the electronic device over a network.

In some embodiments, the sample processing unit includes an opening to permit the user to deposit the biological sample.

In some embodiments, the user is the subject.

In some embodiments, the one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for the at least one target analyte,

In some embodiments, the biological sample includes a soil or food sample.

In some embodiments, the food sample is a dairy sample.

In some embodiments, the dairy sample includes milk.

In some embodiments, the biological sample is a tissue or fluid of a subject

In some embodiments, the tissue or fluid is stool.

In some embodiments, the biological sample is an oral or rectal swab.

In some embodiments, the disease is selected from a plurality of diseases

In some embodiments, the disease is cancer

In some embodiments, the disease is associated with a virus.

In some embodiments, the virus is an RNA virus.

In some embodiments, the virus is a DNA virus.

In some embodiments, the Coxsackie virus is Coxsackie virus A16.

In some embodiments, the pathogenic bacterium is Mycobacterium tuberculosis.

In some embodiments, the pathogenic protozoan is Plasmodium.

In some embodiments, the pathogenic bacterium is Salmonella.

In some embodiments, the plurality of target assays are the same type of assay.

In some embodiments, the amount is a relative amount.

In some embodiments, the footprint is less than or equal to 25 feet².

In some embodiments, the footprint is less than or equal to 9 feet².

In some embodiments, the sample processing unit has a footprint less than or equal to 100 feet².

In some embodiments, the footprint is less than or equal to 25 feet².

In some embodiments, the footprint is less than or equal to 9 feet².

In some embodiments, the sample processing unit is within 5 feet of the electronic device.

In some embodiments, the sample processing unit is within 1 foot of the electronic device.

In some embodiments, the sample processing unit is attached to the electronic device.

In some embodiments, the sample processing unit authenticates the subject.

In some embodiments, the sample processing unit is operatively coupled to the electronic device through the communication interface.

In some embodiments, the authentication unit is part of the electronic device.

In some embodiments, the authentication unit is part of the system.

In another aspect, the present disclosure involves a system for collecting and/or processing a biological sample of a subject, comprising:

a dispensing unit that autonomously dispenses a kit based on a selection provided by a user corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining a presence, absence or amount of at least one target analyte in the biological sample of the subject, wherein the kit comprises (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection； and

a sample processing unit operatively coupled to the dispensing unit, wherein the sample processing unit (a) receives the biological sample collected from the subject using the kit, and (b) processes the biological sample based on the selection inputted by the user corresponding to the at least one target assay from the plurality of target assays, to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In some embodiments, the dispensing unit and the sample processing unit are in a housing.

In some embodiments, the housing has a footprint less than or equal to 100 feet².

In some embodiments, the footprint is less than or equal to 25 feet².

In some embodiments, the footprint is less than or equal to 9 feet².

In some embodiments, the kit comprises (i) a sample collection unit for collecting the biological sample of the subject, and (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the actuator is a robotic arm.

In some embodiments, the system further comprises an electronic device operatively coupled to the dispensing unit, wherein the electronic device provides the selection to the dispensing unit.

In some embodiments, the kit includes a finger prick.

In some embodiments, the kit includes a swap.

In some embodiments, the identifying information is anonymous.

In some embodiments, the identifying information is on a barcode.

In some embodiments, the user is the subject.

In some embodiments, the sample processing unit receives the biological sample in the sample collection unit.

In some embodiments, the sample collection unit includes a cap

In some embodiments, the identifying information is anonymous.

In some embodiments, the identifying information is on a barcode.

In some embodiments, the plurality of target assays are the same type of assay.

In some embodiments, the amount is a relative amount.

In some embodiments, the footprint is less than or equal to 25 feet².

In some embodiments, the footprint is less than or equal to 9 feet².

In some embodiments, the sample processing unit is within 5 feet of the dispensing unit

In some embodiments, the sample processing unit is within 1 foot of the dispensing unit.

In some embodiments, the sample processing unit is attached to the dispensing unit

In some embodiments, the sample collection unit is selected based on a type of the biological sample

In another aspect, the present disclosure involves a system for collecting a biological sample of a subject, comprising:

one or more computer processors that are individually or collectively programmed to (i) authenticate the subject from which the biological sample is to be collected, and (ii) receive a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in the biological sample of the subject； and

a dispensing unit operatively coupled to the one or more computer processors, wherein the dispensing unit, upon authentication of the subject, autonomously directs dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the method further comprises an authentication unit operatively coupled to the one or more computer processors, wherein the authentication unit authenticates the user.

In some embodiments, the sample collection unit and/or one or more reagents are included in a kit.

In some embodiments, the kit includes a finger prick.

In some embodiments, the kit includes a swap.

In some embodiments, the method further comprises a sample processing unit that (1) receives the biological sample collected of the subject, and (2) processes the biological sample based on the at least one target assay to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In some embodiments, the identifying information is anonymous.

In some embodiments, the identifying information is on a barcode.

In some embodiments, the user is the subject.

In some embodiments, the user is a healthcare provider of the subject

In another aspect, the present disclosure involves a method for collecting a biological sample of a subject, comprising:

establishing communication between a dispensing unit and an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in the biological sample of the subject；

receiving the selection inputted by the user in the display of the electronic device； and

using the dispensing unit to direct dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the method further comprises receiving the biological sample collected from the subject at a sample processing unit that processes the biological sample based on the at least one target assay to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In some embodiments, the kit includes a finger prick.

In some embodiments, the kit includes a swap.

In some embodiments, the kit is among a plurality of kits.

In some embodiments, the method further comprises monitoring a quantity of the plurality of kits or a subset thereof, and providing a notification when the quantity approaches or is below a threshold.

In some embodiments, the identifying information is anonymous.

In some embodiments, the identifying information is on a barcode.

In some embodiments, the user is the subject.

In some embodiments, the biological sample includes a soil or food sample.

In some embodiments, the biological sample is a tissue or fluid of a subject.

In some embodiments, the plurality of target assays are the same type of assay.

In some embodiments, the amount is a relative amount.

In another aspect, the present disclosure involves a method for processing a biological sample of a subject, comprising:

activating a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in a biological sample of a subject；

receiving the selection inputted by the user in the user interface； and

transmitting the selection to a dispensing unit that directs dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the one or more graphical elements are part of a questionnaire displayed on the user interface.

In some embodiments, the method further comprises using the questionnaire to (i) provide one or more questions to the user and (ii) generate an output based on one or more responses of the user to the one or more questions, which output corresponds to the at least one target assay from the plurality of target assays.

In some embodiments, the questionnaire is a guided questionnaire.

In some embodiments, the method further comprises capturing a characteristic of the subject using a sensing unit and providing the characteristic to the user.

In some embodiments, the method further comprises receiving the selection inputted by the user subsequent to the user being provided the characteristic of the subject.

establishing communication between a sample processing unit and an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining a presence, absence or amount of at least one target analyte in the biological sample of the subject；

receiving the biological sample from the subject at the sample processing unit； and

using the sample processing unit to process the biological sample based on the selection inputted by the user corresponding to the at least one target assay from the plurality of target assays, to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In some embodiments, the method further comprises using a dispensing unit to dispense a kit based on the selection, wherein the kit comprises (i) a sample collection unit for collecting the biological sample of the subject, and (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the sample collection unit includes a cap.

In some embodiments, the identifying information is anonymous.

In some embodiments, the identifying information is on a barcode.

In some embodiments, the biological sample includes a soil or food sample.

In some embodiments, the biological sample is a tissue or fluid of a subject.

In some embodiments, the plurality of target assays are the same type of assay.

In some embodiments, the amount is a relative amount.

In another aspect, the present disclosure involves a method for collecting and/or processing a biological sample of a subject, comprising:

using a dispensing unit to dispense a kit based on a selection provided by a user corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining a presence, absence or amount of at least one target analyte in the biological sample of the subject, wherein the kit comprises (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection； and

receiving the biological sample collected from the subject using the kit at a sample processing unit operatively coupled to the dispensing unit； and

In some embodiments, the method further comprises directing the selection from an electronic device to the dispensing unit.

In some embodiments, the kit includes a finger prick.

In some embodiments, the kit includes a swap.

In some embodiments, the user is the subject.

In some embodiments, the one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for the at least one target analyte ,

In some embodiments, the plurality of target assays are the same type of assay.

In some embodiments, the amount is a relative amount.

authenticating the subject from which the biological sample is to be collected；

receiving a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in the biological sample of the subject； and

upon authenticating the subject, using a dispensing unit to autonomously direct dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the biological sample includes a soil or food sample.

In some embodiments, the food sample is a dairy sample.

In some embodiments, the dairy sample includes milk.

In some embodiments, the biological sample is a tissue or fluid of a subject.

In some embodiments, the tissue or fluid is stool.

In some embodiments, the biological sample is an oral or rectal swab.

In some embodiments, the sample collection unit includes a cap.

Additional aspects and advantages of the present disclosure will become readily apparent to those skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings (also “Figure” and “Fig. ” herein) , of which:

Figs. 1A-D are schematic diagrams of systems of the present disclosure.

Figs. 2A-B are schematic diagrams illustrating layouts of systems of the present disclosure.

Fig. 3 represents flow charts illustrating operation of exemplary systems of the present disclosure.

Fig. 4 is a schematic diagram of the front panel of an electronic device of the present disclosure.

Fig. 5 is a schematic diagram of the front panel of an electronic device of the present disclosure.

Fig. 6 illustrates an exemplary user interface prompting authentication of identity.

Fig. 7 illustrates an exemplary user interface prompting selection of an assay.

Fig. 8 illustrates an exemplary user interface prompting selection of payment.

Fig. 9 is a schematic diagram of a payment and authentication module of the present disclosure.

Fig. 10 is a schematic diagram illustrating the layout of the front panel of the dispensing unit of the present disclosure.

Fig. 11 is a schematic diagram illustrating the layout of the front panel of a housing comprising both the dispensing unit and the sample processing unit of the present disclosure.

Fig. 12 is a schematic diagram of a sample receiving element of the present disclosure.

Figs. 13A-F represent an exemplary integrated sample collection, processing and analysis system in a front view (Fig. 13A) , an top view (Fig. 13B) , a back view (Fig. 13C) , a right view (Fig. 13D) , a left view (Fig. 13E) , and a top right three quarter view (Fig. 13F) .

Fig. 14 represents various configurations of exemplary integrated sample collection, processing and analysis systems of the present disclosure.

Fig. 15 is a front view of an exemplary electronic device of the present disclosure.

Fig. 16 is a top right three quarter view of a portion of a dispensing unit of the present disclosure.

Figs. 17A and 17B represent an exemplary sample processing unit of the present disclosure in the front view (Fig. 17A) and top right three quarter view (Fig. 17B) .

Figs. 18A-D represent a sample processing unit of the present disclosure with the back of its housing rotated out almost 90 degree in the front top right three quarter view (Fig. 18A) , the back top right three quarter view (Fig. 18B) , the right view (Fig. 18C) and the back view (Fig. 18D) .

Fig. 19 depicts a process of dispensing a commodity, such as a sample collection unit or kit.

Fig. 20 depicts a process by which the sample processing unit may receive the sample collection unit.

Fig. 21 depicts a process by which the sample processing unit may dispense a reactant vessel.

Fig. 22 depicts a process by which the sample processing unit may engage the sample collection unit to the reactant vessel.

Fig. 23 depicts a process by which the sample processing unit may store the sample collection unit together with the reactant vessel.

Fig. 24 depicts a process by which the sample processing unit may move the undetected sample from the upper deck to the lower deck for detection.

Fig. 25 depicts a process by which the sample processing unit may detect the sample.

Fig. 26 depicts the process by which the detected sample may be recovered.

Figs. 27A-G depict a sample collection unit for solid and the process by which the solid sample may be collected.

Figs. 28A-G depict a sample collection unit for liquid and the process by which the liquid sample may be collected.

Figs. 29A-I depict a sample collection unit for swab and the process by which the swab sample may be collected.

Fig. 30 shows a computer control system that is programmed or otherwise configured to implement methods provided herein.

DETAILED DESCRIPTION

While various embodiments of the invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions may occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed.

As used in the specification and claims, the singular forms “a” , “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “amolecule” includes a plurality of molecules, including mixtures thereof.

As used herein, the terms “amplifying” and “amplification” are used interchangeably and generally refer to generating one or more copies or “amplified product” of a nucleic acid. The term deoxyribonucleic acid (DNA) amplification generally refers to generating one or more copies of a DNA molecule or “amplified DNA product” . The term “reverse transcription amplification” generally refers to the generation of DNA from a ribonucleic acid (RNA) template via the action of a reverse transcriptase.

As used herein, the term “cycle threshold” or “Ct” generally refers to the cycle during thermocycling in which an increase in a detectable signal due to amplified product reaches a statistically significant level above background signal.

As used herein, the terms “denaturing” and “denaturation” are used interchangeably and generally refer to the full or partial unwinding of the helical structure of a double-stranded nucleic acid, and in some cases the unwinding of the secondary structure of a single stranded nucleic acid. Denaturation may include the inactivation of the cell wall (s) of a pathogen or the shell of a virus, and the inactivation of the protein (s) of inhibitors. Conditions at which denaturation may occur include a “denaturation temperature” that generally refers to a temperature at which denaturation is permitted to occur and a “denaturation duration” that generally refers to an amount of time allotted for denaturation to occur.

As used herein, the term “elongation” generally refers to the incorporation of nucleotides to a nucleic acid in a template directed fashion. Elongation may occur via the aid of an enzyme, such as, for example, a polymerase or reverse transcriptase. Conditions at which elongation may occur include an “elongation temperature” that generally refers to a temperature at which elongation is permitted to occur and an “elongation duration” that generally refers to an amount of time allotted for elongation to occur.

As used herein, the term “nucleic acid” generally refers to a polymeric form of nucleotides of any length, either deoxyribonucleotides (dNTPs) or ribonucleotides (rNTPs) , or analogs thereof. Nucleic acids may have any three dimensional structure, and may perform any function, known or unknown. Non-limiting examples of nucleic acids include DNA, RNA, coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA) , transfer RNA, ribosomal RNA, short interfering RNA (siRNA) , short-hairpin RNA (shRNA) , micro-RNA (miRNA) , ribozymes, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A nucleic acid may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be made before or after assembly of the nucleic acid. The sequence of nucleotides of a nucleic acid may be interrupted by non-nucleotide components. A nucleic acid may be further modified after polymerization, such as by conjugation or binding with a reporter agent.

As used herein, the term “primer extension reaction” generally refers to the denaturing of a double-stranded nucleic acid, binding of a primer to one or both strands of the denatured nucleic acid, followed by elongation of the primer (s) .

As used herein, the term “reaction mixture” generally refers to a composition comprising reagents necessary to complete nucleic acid amplification (e.g., DNA amplification, RNA amplification) , with non-limiting examples of such reagents that include primer sets having specificity for target RNA or target DNA, DNA produced from reverse transcription of RNA, a DNA polymerase, a reverse transcriptase (e.g., for reverse transcription of RNA) , suitable buffers (including zwitterionic buffers) , co-factors (e.g., divalent and monovalent cations) , dNTPs, and other enzymes (e.g., uracil-DNA glycosylase (UNG) ) , etc) . In some cases, reaction mixtures can also comprise one or more reporter agents.

As used herein, a “reporter agent” generally refers to a composition that yields a detectable signal, the presence or absence of which can be used to detect the presence of amplified product.

As used herein, the term “target nucleic acid” generally refers to a nucleic acid molecule in a starting population of nucleic acid molecules having a nucleotide sequence whose presence, amount, and/or sequence, or changes in one or more of these, are desired to be determined. A target nucleic acid may be any type of nucleic acid, including DNA, RNA, and analogues thereof. As used herein, a “target ribonucleic acid (RNA) ” generally refers to a target nucleic acid that is RNA. As used herein, a “target deoxyribonucleic acid (DNA) ” generally refers to a target nucleic acid that is DNA.

As used herein, the term “subject, ” generally refers to an entity or a medium that has testable or detectable genetic information. A subject can be a person or individual. A subject can be a vertebrate, such as, for example, a mammal. Non-limiting examples of mammals include murines, simians, humans, farm animals, sport animals, and pets. Other examples of subjects include, for example, food, plant, soil, and water.

As used herein, the term “sample” generally refers to any sample that can be assayed by the system or method of the present disclosure. For example, a subject sample may be a biological sample containing one or more nucleic acid molecules. The biological sample may be obtained (e.g., extracted or isolated) from a bodily sample of a subject that may be selected from blood (e.g., whole blood) , plasma, serum, urine, saliva, mucosal excretions, sputum, stool and tears. The bodily sample may be a fluid or tissue sample (e.g., skin sample) of the subject. In some examples, the sample is obtained from a cell-free bodily fluid of the subject, such as whole blood. In such instance, the sample can include cell-free DNA and/or cell-free RNA. In some other examples, the sample is an environmental sample (e.g., soil, waste, ambient air and etc. ) , industrial sample (e.g., samples from any industrial processes) , and food samples (e.g., dairy products, vegetable products, and meat products) .

In some embodiments, a sample is obtained directly from a subject without further processing. In some embodiments, a sample is processed prior to a biological or chemical reaction (e.g., nucleic acid amplification) . For example, a lysis agent may be added to a sample holder prior to adding a biological sample and reagents necessary for nucleic acid amplification. Examples of the lysis agent include Tris-HCl, EDTA, detergents (e.g., Triton X-100, SDS) , lysozyme, glucolase, proteinase E, viral endolysins, exolysins, zymolyase, lyticase, proteinase K, endolysins and exolysins from bacteriophages, endolysins from bacteriophage PM2, endolysins from the B. subtilis bacteriophage PBSX, endolysins from Lactobacillus prophages Lj928, Lj965, bacteriophage 15 Phiadh, endolysin from the Streptococcus pneumoniae bacteriophage Cp-I, bifunctional peptidoglycan lysin of Streptococcus agalactiae bacteriophage B30, endolysins and exolysins from prophage bacteria, endolysins from Listeria bacteriophages, holin-endolysin, cell 20 lysis genes, holWMY Staphylococcus wameri M phage varphiWMY, Iy5WMY of the Staphylococcus wameri M phage varphiWMY, Tween 20, PEG, KOH, NaCl, and combinations thereof. In some embodiments, a lysis agent is sodium hydroxide (NaOH) . In some embodiments, the biological sample is not treated with a detergent.

In some embodiments, the sample is purified (e.g., by filtration, centrifugation, column purification and/or magnetic purification, for example, by using magnetic beads (e.g., super paramagnetic beads) ) to obtain purified nucleic acids. Alternatively, the sample may not be purified

A sample may be of any suitable size or volume. In some examples, a small volume comprises no more than about 5 mL； no more than about 4 mL； no more than about 3 mL； no more than about 2 mL； no more than about 1 mL； no more than about 500 μL； no more than about 250 μL； no more than about 100 μL； no more than about 90 μL； no more than about 80 μL； no more than about 70 μL； no more than about 60 μL； no more than about 50 μL； no more than about 40 μL； no more than about 30 μL； no more than about 25 μL； no more than about 20 μL； no more than about 15 μL； no more than about 10 μL； no more than about 8 μL； no more than about 6 μL； no more than about 5 μL； no more than about 4 μL； no more than about 3 μL； no more than about 2 μL； no more than about 1 μL； no more than about 0.8 μL； no more than about 0.5 μL； no more than about 0.3 μL； no more than about 0.2 μL； no more than about 0.1 μL； no more than about 0.05 μL； or no more than about 0.01 μL.

As used herein, the term “bodily fluid” generally refers to any fluid obtainable from a subject. A bodily fluid may include but not limited to, e.g. blood, urine, saliva, tears, sweat, a bodily secretion, a bodily excretion, or any other fluid originating in or obtainable from a subject. In particular, bodily fluids include but not limited to blood, serum, plasma, bone marrow, saliva, urine, gastric fluid, spinal fluid, tears, stool, mucus, sweat, earwax, oil, glandular secretions, cerebral spinal fluid, semen, vaginal fluid, interstitial fluids derived from tumorous tissue, ocular fluids, placental fluid, amniotic fluid, cord blood, lymphatic fluids, cavity fluids, sputum, pus, meconium, breast milk and/or other secretions or excretions.

As used herein, the term “user” may be a subject from which biological samples are obtained and analyzed. Alternatively, the user may be a healthcare professional. Non-limiting examples of health-care professionals include medical personnel, clinicians (e.g., doctors, nurse practitioners (PACs) , nurses, medical assistants, physical therapists, medical interns, medical technicians) , laboratory personnel (e.g., hospital laboratory technicians, research scientists, pharmaceutical scientists) , a clinical monitor for a clinical trial, an employee of a hospital or health system, an employee of a health insurance company, an employee of a pharmaceutical company, a public health worker, a humanitarian aid worker, or others in the health care industry.

Systems

In an aspect, the present disclosure provides a system for collecting and/or processing a biological sample of a subject. The system may comprise a communication interface in communication with an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining presence, absence or amount of at least one target analyte in the biological sample of the subject. The system may further comprise a dispensing unit comprising one or more computer processors operatively coupled to the communication interface. The one or more computer processors may be individually or collectively programmed to (a) receive the selection inputted by the user in the display of the electronic device, and (b) direct dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In another aspect, the present disclosure provides a system for processing a biological sample of a subject. The system may comprise a communication interface in communication with an electronic device and a dispensing unit. The electronic device may comprise a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining a presence, absence or amount of at least one target analyte in the biological sample of the subject. The dispensing unit may dispense a kit based on the selection. The kit may comprise (1) a sample collection unit for collecting the biological sample of the subject, and (2) one or more reagents necessary for processing the biological sample of the subject based on the selection. The system may further comprise a sample processing unit operatively coupled to the communication interface. The sample processing unit may (a) receives the biological sample of the subject, and (b) processes the biological sample based on the selection inputted by the user corresponding to the at least one target assay from the plurality of target assays, to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In another aspect, the present disclosure provides a system for collecting and/or processing a biological sample of a subject. The system may comprise a dispensing unit. The dispensing unit may autonomously dispense a kit based on a selection provided by a user corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining a presence, absence or amount of at least one target analyte in the biological sample of the subject. The kit may comprise (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

The system may further comprise a sample processing unit operatively coupled to the dispensing unit. The sample processing unit may (a) receive the biological sample collected from the subject using the kit, and (b) process the biological sample based on the selection inputted by the user corresponding to the at least one target assay from the plurality of target assays, to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In another aspect, the present disclosure provides a system for collecting a biological sample of a subject. The system may comprise one or more computer processors. The one or more computer processors may be individually or collectively programmed to (i) authenticate the subject from which the biological sample is to be collected, and (ii) receive a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining presence, absence or amount of at least one target analyte in the biological sample of the subject. The system may further comprise a dispensing unit operatively coupled to the one or more computer processors. The dispensing unit, upon authentication of the subject, may autonomously direct dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

The amount may be a relative amount. For example, the amount may be with reference to a control or baseline amount. The control may be a healthy or normal control. The control may be an abnormal control. As an alternative, the amount is an absolute amount.

Fig. 1A-D illustrate certain system configurations according to various aspects of the present disclosure. The system may comprise an electronic device 101, a communication interface 102, a dispensing unit 103, a sample processing unit 104, and/or an authentication unit 105. Fig. 1A illustrates a system comprising an electronic device 101, a communication interface 102, and a dispensing unit 103. Fig. 1B illustrates a system comprising an electronic device 101, a communication interface 102, a dispensing unit 103, and a sample processing unit 104. Fig. 1C illustrates a system comprising a dispensing unit 103 and a sample processing unit 104. Fig. 1D illustrates a system comprising a dispensing unit 103 and an authentication unit 105.

Alternatively, system configurations with other combinations of the aforesaid components may also be contemplated. A skilled artisan shall understand that the present disclosure is not limited to the configuration as described above. For example, the authentication unit may be added to any configuration as illustrates in Fig. 1A-C to allow authentication of the user.

In some embodiments, the system further comprises a payment unit enabling payment by the user. In some embodiments, the payment unit is integral to the authentication unit. In some embodiments, the payment unit is a discrete unit.

Any of the system components as described above may contain one or more computer processors for carrying out or assisting their respective functions. The one or more computer processors may be any computer processor as described elsewhere herein. For example, the computer processor may be a single core or multi core processor, or a plurality of processors for parallel processing.

As shown in Fig. 2, the system of the present disclosure may comprise an electronic device 101 and a dispensing unit 103. The electronic device and the dispensing unit may be connected via a communication interface (not shown) . The electronic device 101 and the dispensing unit 103 may be juxtaposed as shown in Fig. 2A, but their positions are not limited thereto. The electronic device 101 and the dispensing unit 103 may be stacked, or integrated within one housing. The electronic device 101 and the dispensing unit 103 may be deployed in any positional relationship as long as the two elements are in communication with each other, in some cases via a communication interface, such that a user may actuate the dispensing unit 103 by operating on the electronic device 101.

In some embodiments, the dispensing unit 103 in Fig. 2A is also a sample processing unit.

As shown in Fig. 2B, the system of the present disclosure may comprise an electronic device 101, a dispensing unit 103, and a sample processing unit 104. The electronic device, the dispensing unit, and the sample processing unit may be connected to one another via a communication interface (not shown) . The electronic device 101, the dispensing unit 103, and the sample processing unit 104 may be juxtaposed as shown in Fig. 2B, but their positions are not limited thereto. The electronic device 101, the dispensing unit 103, and the sample processing unit 104 may be stacked, or two among them may be stacked and juxtaposed with the other, or two among them may be juxtaposed and staked with the other, or any two or all of the three may be integrated within one housing. The electronic device 101, the dispensing unit 103, and the sample processing unit 104 may be deployed in any positional relationship as long as the three elements are in communication with one another, in some cases via a communication interface, such that a user may actuate the dispensing unit 103 and/or the sample processing unit 104 by operating on the electronic device 101.

In various aspects, the system may comprise an input module that receives a user request to amplify a target nucleic acid (e.g., target RNA, target DNA) present in a biological sample obtained direct from a subject. Any suitable module capable of accepting such a user request may be used. The input module may comprise, for example, a device that comprises one or more processors. Non-limiting examples of devices that comprise processors (e.g., computer processors) include a desktop computer, a laptop computer, a tablet computer (e.g.,

iPad,

Galaxy Tab) , a cell phone, a smart phone (e.g.,

iPhone,

enabled phone) , a personal digital assistant (PDA) , a video-game console, a television, a music playback device (e.g., iPod) , a video playback device, a pager, and a calculator. Processors may be associated with one or more controllers, calculation units, and/or other units of a computer system, or implanted in firmware as desired. If implemented in software, the routines (or programs) may be stored in any computer readable memory such as in RAM, ROM, flash memory, a magnetic disk, a laser disk, or other storage medium. Likewise, this software may be delivered to a device via a delivery method including, for example, over a communication channel such as a telephone line, the internet, a local intranet, a wireless connection, etc., or via a transportable medium, such as a computer readable disk, flash drive, etc. The various steps may be implemented as various blocks, operations, tools, modules or techniques which, in turn, may be implemented in hardware, firmware, software, or any combination thereof. When implemented in hardware, some or all of the blocks, operations, techniques, etc. may be implemented in, for example, a custom integrated circuit (IC) , an application specific integrated circuit (ASIC) , a field programmable logic array (FPGA) , a programmable logic array (PLA) , etc.

In some embodiments, the input module is configured to receive a user request to perform amplification of the target nucleic acid. The input module may receive the user request directly (e.g., by way of an input device such as a keyboard, mouse, or touch screen operated by the user) or indirectly (e.g., through a wired or wireless connection, including over the internet) . Via output electronics, the input module may provide the user’s request to the amplification module. In some embodiments, an input module may include a user interface (UI) , such as a graphical user interface (GUI) , that is configured to enable a user provide a request to amplify the target nucleic acid. A GUI can include textual, graphical and/or audio components. A GUI can be provided on an electronic display, including the display of a device comprising a computer processor. Such a display may include a resistive or capacitive touch screen.

Non-limiting examples of users include the subject from which the biological sample was obtained, medical personnel, clinicians (e.g., doctors, nurses, and laboratory technicians) , laboratory personnel (e.g., hospital laboratory technicians, research scientists, and pharmaceutical scientists) , and a clinical monitor for a clinical trial, or others in the health care industry.

In various aspects, the system comprises an amplification module for performing nucleic acid amplification reaction on target nucleic acid or a portion thereof, in response to a user request received by the input module. The amplification module may be capable of executing any of the methods described herein and may include any of a fluid handling device, one or more thermocyclers, a device or module for receiving one or more reaction vessels (e.g., wells of a thermal block of a thermocycler) , a detector (e.g., optical detector, spectroscopic detector, electrochemical detector) capable of detecting amplified product, and a device or module for outputting information (e.g., raw data, processed data, or any other type of information described herein) regarding the presence and/or amount of amplified product (e.g., amplified DNA product) to a recipient. In some cases, the amplification module may comprise a device with a computer processor as described elsewhere herein and may also be capable of analyzing raw data from detection, with the aid of appropriate software. Moreover, in some embodiments, the amplification module may comprise input electronics necessary to receive instructions from the input module and may comprise output electronics necessary to communicate with the output module.

In some embodiments, one or more steps of providing materials to a reaction vessel, amplification of nucleic acids, detection of amplified product, and outputting information may be automated by the amplification module. In some embodiments, automation may comprise the use of one or more fluid handlers and associated software. Several commercially available fluid handling systems can be utilized to run the automation of such processes. Non-limiting examples of such fluid handlers include fluid handlers from Perkin-Elmer, Caliper Life Sciences, Tecan, Eppendorf, Apricot Design, and Velocity 11.

In some embodiments, an amplification module may include a real-time detection instrument. Non-limiting examples of such instruments include a real-time PCR thermocycler, ABI

7000 Sequence Detection System, ABI

7700 Sequence Detection System, Applied Biosystems 7300 Real-Time PCR System, Applied Biosystems 7500 Real-Time PCR System, Applied Biosystems 7900 HT Fast Real-Time PCR System (all from Applied Biosystems) ； LightCycler^TM System (Roche Diagnostics GmbH) ； Mx3000P^TM Real-Time PCR System, Mx3005P^TM Real-Time PCR System, and

Multiplex Quantitative PCR System (Stratagene, La Jolla, Calif. ) ； and Smart Cycler System (Cepheid, distributed by Fisher Scientific) . In some embodiments, an amplification module may comprise another automated instrument such as, for example, a

system (Roche Molecular Systems) , a TIGRIS DTS system (Hologic Gen-Probe, San Diego, CA) , a PANTHER system (Hologic Gen-Probe, San Diego, CA) , a BD MAX^TM system (Becton Dickinson) , a GeneXpert System (Cepheid) , a

(BioFire Diagnostics) system, an iCubate system, an IDBox system (Luminex) , an EncompassMDx^TM (Rheonix) system, a Liat^TM Aanlyzer (IQuum) system, a Biocartis’Molecular Diagnostic Platform system, an

ML system (Enigma Diagnostics) , a

system (T2 Biosystems) , a

system (NanoSphere) , a Great Basin’s Diagnostic System, a Unyvero^TM System (Curetis) , a PanNAT system (Micronics) , or a Spartan^TM RX system (Spartan Bioscience) .

In various aspects, the system may comprise an output module operatively connected to the amplification module. In some embodiments the output module may comprise a device with a processor as described above for the input module. The output module may include input devices as described herein and/or may comprise input electronics for communication with the amplification module. In some embodiments, the output module may be an electronic display, in some cases the electronic display comprising a UI. In some embodiments, the output module is a communication interface operatively coupled to a computer network such as, for example, the internet. In some embodiments, the output module may transmit information to a recipient at a local or remote location using any suitable communication medium, including a computer network, a wireless network, a local intranet, or the internet. In some embodiments, the output module is capable of analyzing data received from the amplification module. In some cases, the output module includes a report generator capable of generating a report and transmitting the report to a recipient, wherein the report contains any information regarding the amount and/or presence of amplified product as described elsewhere herein. In some embodiments, the output module may transmit information automatically in response to information received from the amplification module, such as in the form of raw data or data analysis performed by software included in the amplification module. Alternatively, the output module may transmit information after receiving instructions from a user. Information transmitted by the output module may be viewed electronically or printed from a printer.

One or more of the input module, biological sample treatment module, amplification module, and output module may be contained within the same device or may comprise one or more of the same components. For example, an amplification module may also comprise an input module, a biological sample treatment module, an output module, or two or more of them. In other examples, a device comprising a processor may be included in both the input module and the output module. A user may use the device to request that a target nucleic acid be amplified and may also be used to transmit information regarding amplified product to a recipient. In some cases, a device comprising a processor may be included in all four modules, such that the device comprising a processor may also be used to control, provide instructions to, and receive information back from instrumentation (e.g., a thermocycler, a detector, an incubator, a fluid handling device) included in the amplification module or any other module.

Methods

In another aspect, the present disclosure provides a method for collecting a biological sample of a subject. The method may comprise establishing communication between a dispensing unit and an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining presence, absence or amount of at least one target analyte in the biological sample of the subject. The amount may be a relative amount. The method may further comprise receiving the selection inputted by the user in the display of the electronic device. The method may further comprise using the dispensing unit to direct dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the method may further comprise receiving the biological sample collected from the subject at a sample processing unit that processes the biological sample based on the at least one target assay to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In another aspect, the present disclosure provides a method for processing a biological sample of a subject. The method may comprise activating a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining presence, absence or amount of at least one target analyte in a biological sample of a subject. The amount may be a relative amount. The method may further comprise receiving the selection inputted by the user in the user interface. The method may further comprise transmitting the selection to a dispensing unit that directs dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the method further comprises capturing a characteristic of the subject using a sensing unit and providing the characteristic to the user. In some embodiments, the characteristic may be a sound, image or video having the subject. If the characteristic is an image or a video, the sensing unit may be a camera, a digital camera, a video recorder, a camcorder, a smartphone or tablet computer having a camera or video recorder functionality, and the like, and/or the characteristic may be provided to the user by an electronic display such as a monitor, a television, a tablet computer screen, a mobile device screen, and the like. If the characteristic is a sound, the sensing unit may be a microphone, a smartphone or tablet computer having a microphone functionality, and the like, and/or the characteristic may be provided to the user via a speaker, a headphone, a blue tooth earphone, and the like. Alternatively, the characteristic may be a temperature, resistance, impedance, capacitance, luminescence, or fluorescence of the subject. Accordingly, the sensing unit may be an electrochemical sensor, an optical sensor, an electronic sensor, a piezoelectric sensor, a gravimetric sensor, a pyroelectric sensor, and the like, and/or the characteristic may be provided to the user as a report as described elsewhere herein, for example, provided to the user as a printed report or an electronic report, the latter could be via an electronic display such as a monitor, a television, a tablet computer screen, a mobile device screen, and the like.

In some embodiments, the method further comprises receiving the selection inputted by the user subsequent to the user being provided the characteristic of the subject. The user may input the selection as described elsewhere herein. For example, the user may input the selection by touching one of various options displayed on a touchscreen. Alternatively, the user may input the selection by an input module. Furthermore, the user may input the selection remotely via a user terminal.

In some embodiments, the characteristic is a sound, image or video of the subject. The sound, image or video may be captured by a sensing unit as described elsewhere herein. The sensing unit may be integrated in the system as described elsewhere herein.

In some embodiments, the characteristic is a temperature, resistance, impedance, capacitance of the subject. The temperature, resistance, impedance, capacitance may be captured by a sensing unit as described elsewhere herein. Alternatively, the characteristic may be luminescence or fluorescence of the subject. For example, specific luminescent or fluorescent “markings” may be made onto the body of the subject in advance to allow the subject characterized by the such “markings” upon captured by the sensing unit. The sensing unit may be integrated in the system as described elsewhere herein.

In another aspect, the present disclosure provides a method for processing a biological sample of a subject. The method may comprise establishing communication between a sample processing unit and an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining a presence, absence or amount of at least one target analyte in the biological sample of the subject. The method may further comprise receiving the biological sample from the subject at the sample processing unit. The method may further comprise using the sample processing unit to process the biological sample based on the selection inputted by the user corresponding to the at least one target assay from the plurality of target assays, to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In some embodiments, the method further comprises using a dispensing unit to dispense a kit based on the selection. The kit may comprise (i) a sample collection unit for collecting the biological sample of the subject, and (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In another aspect, the present disclosure provides a method for collecting and/or processing a biological sample of a subject. The method may comprise using a dispensing unit to dispense a kit based on a selection provided by a user corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining a presence, absence or amount of at least one target analyte in the biological sample of the subject. The kit may comprise (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection. The method may further comprise receiving the biological sample collected from the subject using the kit at a sample processing unit operatively coupled to the dispensing unit. The method may further comprise using the sample processing unit to process the biological sample based on the selection inputted by the user corresponding to the at least one target assay from the plurality of target assays, to determine the presence, absence or amount of the at least one target analyte in the biological sample of the subject.

In some embodiments, the method further comprises directing the selection from an electronic device to the dispensing unit. The selection may be transmitted from the electronic device to the dispensing unit via a communication interface as described elsewhere herein. In some cases, the transmission via the communication interface may be performed via a wired or a wireless connection.

In another aspect, the present disclosure provides a method for collecting a biological sample of a subject. The method may comprise authenticating the subject from which the biological sample is to be collected. The method may further comprise receiving a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining presence, absence or amount of at least one target analyte in the biological sample of the subject. The method may further comprise, upon authenticating the subject, using a dispensing unit to autonomously direct dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection

During operation of an embodiment of the system according to the present disclosure, a user may use an input module to place request of a transaction on the electronic device, and, optionally, provide authentication and/or payment information via an authentication unit and/or a payment unit. Via the input module and a display device the user may interact with a user terminal associated with the electronic device such that proper information and request are provided to the electronic device, in some cases to one or more computer processors comprised in the electronic device. Upon verifying of the authenticity and accuracy of the aforesaid information and deciding that the user request matches the provided information, the electronic device, in some cases the one or more computer processors comprised in the electronic device may validate the transaction by actuating the dispensing unit to dispense the commodity requested by the user, in some cases a sample collection unit as described elsewhere herein. The electronic device may display or output a report regarding the transaction via an output module.

Fig. 3 shows flow charts of the operation according to an embodiment of the system according to the present disclosure. Fig. 3A illustrates one process for the system of the present disclosure to complete a transaction. In step 301, the identity of the user is authenticated, in some cases using an authentication unit. In step 302, the user selects an assay type, in some cases with an input module. In step 303, the system, in some cases one or more computer processors comprised therein, decides whether the information input in

step

301 and 302 matches each other. If the answer is “yes” , the process proceeds to the next step 304. If the answer is “no” , the process reverts back to the initial step 301. In step 304, the user makes a payment, in some cases via a payment unit. In step 305, the system dispenses a commodity on the basis of the assay type selected in the step 302, thereby completing the transaction.

Fig. 3B illustrates an alternative process for the system of the present disclosure to complete a transaction. The steps 301～305 are virtually identical to those in Fig. 3A, but the order of the

step

301 and 302 are inverted such that the user selects the assay type before the authentication of the user’s identity. Consequently, if in step 303, the answer is “no” , the process reverts back to the initial step 302.

Electronic Devices

In another aspect, the present disclosure provides an electronic device. The electronic device may comprise a display screen. The display screen may have a user interface. The user interface may display one or more graphical elements. The one or more graphical elements may permit a user to input a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining presence, absence or amount of at least one target analyte in a biological sample.

In some embodiments, a user may input selection in a display of the electronic device. For example, the user may input the selection by touching one of various options displayed in a touchscreen.

In some embodiments, a user may input selection in the user interface. For example, the user may input selection by selecting one or more graphical elements in the user interface. For example, the user may input selection remotely by operating on a user interface in remote communication with the system in accordance with the present disclosure.

In some embodiments, the one or more graphical elements may include a plurality of graphical elements. Each of the plurality of graphical elements may correspond to a given target assay among said plurality of target assays.

In some embodiments, the one or more graphical elements may be part of a questionnaire displayed on the user interface. The questionnaire may provide one or more questions to the user. Alternatively or additionally, the questionnaire may generate an output based on one or more responses of the user to the one or more questions. The output may correspond to the at least one target assay from the plurality of target assays.

In some embodiments, the questionnaire may be a guided questionnaire. The questionnaire may guide the user to input the personal information regarding the user and/or the subject. The questionnaire may guide the user to select payment option or assay option. The questionnaire may guide the user to input other information that may be of interest to the operator of the system in accordance with the present disclosure.

The user interface may display instructions for collecting a biological sample from a subject. The display screen may be operatively coupled to one or more computer processors as described elsewhere herein. The display screen may be a capacitive touch screen or resistive touch screen. The one or more graphical elements may permit a user to input a selection of one or more of a tissue type of a biological sample and disease.

In another aspect, the present disclosure provides an electronic device for processing a biological sample of a subject. The electronic device may comprise a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining presence, absence or amount of at least one target analyte in a biological sample of a subject. The electronic device may also comprise one or more computer processors operatively coupled to the display screen. The one or more computer processors may be individually or collectively programmed to (a) receive the selection inputted by the user in the user interface, and (b) transmit the selection to a dispensing unit that directs dispensing of (i) a sample collection unit for collecting the biological sample of the subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the electronic device may be coupled to a dispensing unit as described elsewhere herein. The electronic device may be directly coupled to the dispensing unit. The electronic device may be remoted coupled to the dispensing unit. The electronic device may be operatively coupled to the dispensing unit, in some cases over a network. In some embodiments, the electronic device may provide selection to the dispensing unit.

In some embodiments, the electronic device may be within 5 feet of a dispensing unit as described elsewhere herein. In some embodiments, the electronic device may be within about 30 feet, 15 feet, 10 feet, 5 feet, 4 feet, 3 feet, 2 feet, 1 foot, 0.5 feet, 0.1 feet or directly adjacent to the dispensing unit.

In some embodiments, the electronic device may be attached to the dispensing unit. In some embodiments, the electronic device may be operatively coupled to the dispensing unit through a communication interface as described elsewhere herein. In some embodiments, the electronic device may be in communication with the communication interface, in some cases over a network. In some embodiments, the electronic device may be in communication with the communication interface, in some cases through at least one electronic bus.

In some embodiments, the electronic device may be a mobile electronic device of a user or a subject. In some embodiments, the electronic device may further include a sensing unit as described elsewhere herein. In some embodiments, the electronic device may comprise an authentication unit as a part thereof.

Non-limiting examples of an electronic device include a personal computer (laptop computer, desktop computer, a video game console) , a portable electronic device (e.g., a mobile telephone (e.g., a smartphone or the like capable of running mobile applications (apps) ) , a tablet computer, a pager, a calculator, a portable video game console, a portable music player (e.g., iPod^TM or the like) ) .

The electronic device can be a component of a remote computer system networked with a computer processor as described elsewhere herein. The network can be the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet. In some cases, the network is a cellular phone network that is in communication with the Internet. In some cases, the remote computer system is a part of a decentralized computing network (e.g., a network “cloud” ) comprising the remote computer system and, in some cases, the electronic device.

The user interface can be useful in aiding the use to make selection, make payment, and/or provide authentication information. The user interface can be a component of a display screen of an electronic device, such, as for example, a computer system or other type of electronic device described elsewhere herein. The display screen may be an electronic display. In some cases, an electronic display may include a resistive or capacitive touch screen. The user interface can include one or more graphical elements, such as text, images and/or video. The arrangement of the one or more graphical elements can be tailored to a given questionnaire, instruction, and/or output. The arrangement of the one or more graphical elements may be statically or dynamically tailored for the given questionnaire, instruction, and/or output.

A user interface can be provided on an electronic display, including the display of a device comprising the computer processor. In some cases, the electronic device is a portable electronic device, as described elsewhere herein. Moreover, a user interface can include textual, graphical and/or audio components. A user interface can be provided on an electronic display, including the display of a device comprising a computer processor. Moreover, in some cases, the operation of the system/method of the present disclosure is performed with a notification or alert over the network. Such a notification or alert can be provided to an electronic device described herein, including via text message, via email, via social media and/or via an application usable on the electronic device. Moreover, a notification or alert provided to the user may prompt an administrator, a health care professional, or other authority to take actions with respect to the operation of the system/method of the present disclosure.

In some cases, the user interface can be a user interface of an application run by the electronic device. Where the electronic device is a portable device (e.g., a smartphone, a portable music player, a tablet computer, etc. ) , the application may be a mobile application (an “app” ) that can be run on the portable device. Mobile applications include software that is designed to be run on and/or displayed on a mobile device.

In some cases, a user interface can be a graphical user interface. Moreover, a user interface can include one or more graphical elements. Graphical elements can include image and/or textual information, such as pictures, icons and text. The graphical elements can have various sizes and orientations on the user interface. Furthermore, an electronic display screen may be any suitable electronic display including examples described elsewhere herein. Non-limiting examples of electronic display screens include a cathode ray tube display (CRT) , a light-emitting diode display (LED) , an electroluminescent display (ELD) , an electronic paper or E ink, a plasma display panel (PDP) , a liquid crystal display (LCD) , a high-performance addressing display (HPA) , a thin-film transistor display (TFT) , an organic light-emitting diode display (OLED) , an interferometric modulator display (IMOD) , or a digital microshutter display (DMS) . In some embodiments, an electronic display screen may include a touch screen (e.g., a capacitive or resistive touch screen) such that graphical elements displayed on a user interface of the electronic display screen can be selected via user touch with the electronic display screen.

In some embodiments, the user interface can display a plurality of graphical elements. Among the plurality of graphical elements, one of them may be associated with a message to the user prompting selection, whereas some others may each be associated with a given option among a plurality of options for the selection.

Fig. 4 is a schematic diagram of the front panel of an electronic device 401 according to an embodiment of the present disclosure. Disposed on this front panel of the electronic device 401 are an display screen 412, an output module 413, an input module 414, and a payment/authentication module 415. Please be noted that Fig. 4 is merely an illustration of one possible arrangement of these various elements. It is conceivable to a person skilled in the art that the relative position of these elements may be changed to obtain any other arrangement, as long as such an arrangement makes practical sense.

Fig. 5 is a schematic diagram of the front panel of an electronic device 501 according to an alternative embodiment of the present disclosure. Disposed on this front panel of the electronic device 501 are a display screen/input module 512/514, an output module 513, and a payment/authentication module 515. The arrangement as illustrated in Fig. 5 differs from that in Fig. 4 in that the display screen 512 also doubles as the input module 514. Accordingly, the display screen/input module 512/514 may comprise a touch screen via which the user may input information to the electronic 501.

In some embodiments, the user interface is used to prompt the user to verify his/her identity. An example of an interface prompting authentication of identity is shown in Fig. 6. Displayed on the display screen 612 are several graphical elements 6121 and 6122. The graphical element 6121 may include a message to the user prompting selection of an identity authentication option. For example, the message may read as “Please identify yourself with one of the following options” .

The graphical elements 6122 may include description of various identity authentication options. Non-limiting options for authentication of identity may include fingerprint, biometric identification, biometric card, PIN with/without a user name, barcode or two-dimensional code, and the like. Although Fig. 6 only shows three graphical elements 6122a～c, a person skilled in the art will understand any number of options may be provided and accordingly, the same number of graphical elements 6122 may be presented to the user in the display screen 612.

Upon prompted by the message included in the graphical element 6121, the user may select an option among various available options by selecting one of the graphical elements 6122. The user may make the selection via the input module as described above. Alternatively, the user may make the selection by direct touching one of the graphical element 6122 on the screen if the display screen 612 comprises a touch screen as an input module.

In some embodiments, the user interface is used to prompt the user to select an assay. An example of an interface prompting selection of an assay is shown in Fig. 7. Displayed on the display screen 712 are several graphical elements 7121 and 7122. The graphical element 7121 may include a message to the user prompting selection of an assay. For example, the message may read as “Please select the assay you wish to run” .

The graphical elements 7122 may include description of various assay options. Non-limiting options for assay to be performed may include assays for detecting pathogens, genetic markers, circulating marks, and the like. Although Fig. 7 only shows three graphical elements 7122a～c, a person skilled in the art will understand any number of options may be provided and accordingly, the same number of graphical elements 7122 may be presented to the user in the display screen 712.

Alternatively, the graphical elements 7122 do not present to the user the specific assay to be performed, but rather a disease to be detected. Upon user selection of the specific disease, the electronic device, in some cases the one or more computer processors comprised therein, will automatically determine the specific assay to be performed based on an internal or external database.

In some embodiments, the user interface is used to prompt the user to select a payment option. An example of an interface prompting selection of payment option is shown in Fig. 8. Displayed on the display screen 812 are several graphical elements 8121 and 8122. The graphical element 8121 may include a message to the user prompting selection of a payment option. For example, the message may read as “Please select the method of payment” .

The graphical elements 8122 may include description of various payment options. Non-limiting options for making the payment may include cash, credit card, debit card, pre-paid card, token, smart card, smart phone (Alipay, Wechat pay, apple pay, etc. ) , and the like. Although Fig. 8 only shows three graphical elements 8122a～c, a person skilled in the art will understand any number of options may be provided and accordingly, the same number of graphical elements 8122 may be presented to the user in the electronic display 812.

Upon prompted by the message included in the graphical element 8121, the user may select an option among various available options by selecting one of the graphical elements 8122. The user may make the selection via the input device as described above. Alternatively, the user may make the selection by direct touching one of the graphical element 8122 on the screen if the display screen 812 comprises a touch screen as an input module.

Additionally, the user interface may also provide the user with a questionnaire to assess the identity, prescription, and/or physiological state of the subject； and identifying at least one of suitable target assay from results of the questionnaire. For example, the user may be asked to provide information regarding prescription for the subject as described elsewhere herein along with information regarding the identity of the subject. For example, the user may be asked to provide information regarding physiological state of the subject as described elsewhere herein along with information regarding the identity of the subject. In some embodiments, the user is the subject. In some embodiments, the user is an individual authorized to select and/or obtain the at least one target assay for the subject.

The results of the questionnaire can be used to determine the selection of the at least one target assay (e.g., based on the prescription for the subject or the inputted physiologic states of the subject) . In some cases, the results of a questionnaire can be used to search a database and identify the at least one target assay which is suitable as regards to the prescription and/or the physiologic states of the subject.

In some cases, the method also includes drawing one or more correlation (s) between the results of the questionnaire and the at least one target assay. A non-limiting example of such a correlation includes the prevalence and/or trend of the dispensing of the at least one target assay in a population of subjects identifiable by information submitted in the questionnaire. Such a correlation can be useful in assessing the likelihood of a subject in the population of subjects identifiable by information submitted in the questionnaire has in need of the at least one target assay. In some cases, a determined correlation is stored in a database for future use and comparison with other analyses of the assay use, for example, feedback from subjects or health care professional as to the suitability or utility of the at least target assay in question. Additionally, the results of a questionnaire may also be used to guide the selection of the at least one target assay. Upon using a questionnaire to identify the at least one target assay, specific kits, sample collection unit, and/or reagents, as well as any other necessary consumable can be selected for carrying out the target assay.

Moreover, the questionnaire can be provided to the user on a user interface (e.g., a user interface) of an electronic device and, in some cases, can be used for machine learning purposes. Questionnaire results can be stored on an electronic device that receives answers to the questionnaire from the user or can be transmitted for storage to a remote data storage unit. Machine learning can aid in future processing of biological samples, processing of quantitative measures, analysis of disease information indicative of a progression or regression of a disease state and can also provide information regarding evaluations across multiple subjects. In some cases, the questionnaire can be provided to the subject on the electronic display of electronic device, including a portable electronic device as described elsewhere herein. In some cases, the questionnaire is provided to the subject via a mobile application (e.g., an “app” ) .

Communication Interface

In another aspect, the present disclosure provides a communication interface. The communication interface may allow communication between various components of the system as described elsewhere herein.

Communication may take place as serial communication or parallel communication. In some embodiments, the communication interface may be a serial communication interface. In some embodiments, the communication interface may be a parallel communication interface.

Various serial communication interfaces and/or parallel communication interfaces may be used. Non-limiting serial communication interfaces include those used in serial communication systems such as ARINC 818 Avionics Digital Video Bus, Atari SIO, CoaXPress, Ethernet, Fibre Channel, FireWire, HyperTransport, InfiniBand, I²C, MIL-STD-1553A/B, PCI Express, Profibus, RS-232, RS-422, RS-423, RS-485, SDI-12, Serial ATA, Serial Attached SCSI, SONET and SDH, SpaceWire, SPI, T-1, E-1 and variants, Universal Serial Bus, UNI/O, 1-Wire, etc. Non-limiting parallel communication interfaces include those used in parallel communication systems such as IEEE-488 Parallel (HPIB or GPIB) , Centronics Parallel Protocol, SCSI, IDE, ISA, PCI, AGP, etc.

The communication interface may be in any form as deemed appropriate by a skilled artisan. For example, the communication interface may assume the form of a port, a cable, a connector, a plug, etc. In some embodiments, the communication interface may be a wireless communication interface. The communication interface may assume forms of pin-and-hole configuration, male or female configuration, or any other suitable configurations.

In some embodiments, the communication interface may be in communication with an electronic device as described elsewhere herein. The electronic device may be a portable computer, such as a Smart phone or smart watch. The electronic device may be a desktop computer.

In some embodiments, the communication interface may be operatively coupled to a dispensing unit as described elsewhere herein. The communication interface may be operatively coupled to the dispensing unit wirelessly or through one or more wired interfaces. The communication interface may be operatively coupled to the dispensing unit through a network, such as the Internet or intranet.

In some embodiments, the communication interface may be operatively coupled to a sample processing unit as described elsewhere herein. The communication interface may be operatively coupled to the sample processing unit wirelessly or through one or more wired interfaces. The communication interface may be operatively coupled to the sample processing unit through a network, such as the Internet or intranet.

In some embodiments, the communication interface may be in communication with an electronic device as described elsewhere herein. The communication may be any communication as described elsewhere herein. The communication may be local or remote communication. For example, the communication may be via a communication bus, such as a motherboard. Alternatively, the communication may be via a network, such as the Internet, an internet , an extranet, an intranet, a peer-to-peer network, a telecommunication network, and/or a data network.

In some embodiments, the communication interface may be in communication with an authentication unit as described elsewhere herein. The communication may be any communication as described elsewhere herein. The communication may be local or remote communication. For example, the communication may be via a communication bus, such as a motherboard. Alternatively, the communication may be via a network, such as the Internet, an internet , an extranet, an intranet, a peer-to-peer network, a telecommunication network, and/or a data network.

In some embodiments, the communication interface may bring one or more computer processors as described elsewhere herein in communication with the dispensing unit. The one or more computer processors may be any computer processor as described elsewhere herein. For example, the computer processor may be a single core or multi core processor, or a plurality of processors for parallel processing.

Sample Collection Unit

In another aspect, the present disclosure provides a sample collection unit for collecting a biological sample of a subject. The subject may be any subject as described elsewhere herein. In some cases, the subject may be a person or an individual. In some cases, the subject may be the user himself/herself. The biological sample may be any biological sample as described elsewhere herein. The biological sample may contain nucleic acids such as DNA and/or RNA, proteins such as structural proteins and/or enzymes, lipids, carbohydrates, modified proteins such as glycoproteins and/or lipoproteins, as well as any analytes as described elsewhere herein.

In some embodiments, the sample collection unit may receive the biological sample collected of the subject. Alternatively or additionally, the sample collection unit may process the biological sample based on at least one target assay to determine the presence, absence or amount of at least one target analyte in the biological sample of the subject.

In some embodiments, the sample collection unit may be included in a kit as described elsewhere herein. In some cases, the kit includes the sample collection unit only. In some cases, the kit may include the sample collection unit together with any number of other reagents or materials. The other reagents or materials may be necessary for the sample collection unit to collect sample (s) as described elsewhere herein. In some cases, the kit may include the sample collection unit together with instructions for use of the sample collection unit to collect sample (s) as described elsewhere herein.

In some embodiments, the sample collection unit may include a cap. The cap may allow the collected sample to be enclosed within the sample collection unit. The cap may be permanently associated with the sample collection unit. Alternatively, the cap may be removable from the sample collection unit.

In some embodiments, the sample collection unit may include identifying information of the subject. The identifying information may be anonymous. The identifying information may be on a barcode. The identifying information may be a radio-frequency identification (RFID) tag.

In some embodiments, the sample collection unit may be selected based on a type of the biological sample. The type of the biological sample may include any biological sample as described elsewhere herein. The type of the biological sample may include solid, liquid, blood, swab, etc. Non-limiting examples of solid samples may include stool, biopsy, body tissues, etc. Non-limiting examples of liquid samples may include saliva, urine, and other bodily fluids. The blood sample may be freshly taken from the user or the subject before being collected by the sample collection unit. The swab sample may be freshly collected by the sample collection unit after the swab is brought in contact with a region where a sample of interest may be present.

In some embodiments, the biological sample may be received in a sample processing unit as described elsewhere herein in the sample collection unit. The biological sample may be received via a sample receiving port as described elsewhere herein. The sample receiving port may have a shutter that can be deployed in at least two positions including an open position and a closed position. After received by the sample processing unit, the biological sample may be transferred to a storage element within the sample processing unit as described elsewhere herein, prior to being assayed or transported.

In some embodiment, the sample collection unit may comprise a collection vessel and optionally, a buffer reservoir. In some embodiments, the collection vessel may have a piercing member deposited within it. The buffer reservoir may comprise a membrane such that when the buffer reservoir is in a first position relative to the collection vessel, the membrane stays clear off the piercing member, and when the buffer reservoir is in a second position relative to the collection vessel, the piercing member pierces the membrane to provide a fluid communication between the buffer reservoir and the collection vessel such that the content of the buffer reservoir flows from the buffer reservoir to the collection vessel.

The content of the buffer reservoir may be a dilution buffer, a lysis buffer, or any suitable buffer. The piercing member may comprise needle (s) disposed on it such that when the buffer reservoir is brought to the second position relative to the collection vessel, the needle (s) on the piercing member pierces the membrane of the buffer reservoir to bring the buffer reservoir in fluid communication with the collection vessel. In some embodiments, the needle (s) may be hollow needle (s) . The needle (s) may be of various gauges. In some embodiments, the needle (s) may have a gauge of at least about 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 22s, 23, 24, 25, 26, 26s, 27, 28, 29, 30, 31, 32, 33, or 34. Alternatively, the piercing member may not comprise any needle.

Alternatively or additionally, the buffer reservoir may further comprise an accessory piercing member deposited in it such that when the buffer reservoir is in a first position relative to the collection vessel, the membrane stays clear off the accessory piercing member, and when the buffer reservoir is in a second position relative to the collection vessel, the accessory piercing member pierces the membrane to provide a fluid communication between the buffer reservoir and the collection vessel such that the content of the buffer reservoir flows from the buffer reservoir to the collection vessel. In some embodiments, the accessory piercing member is configured to be proximal to the bottom of the collection vessel as compared to the membrane when the buffer reservoir is fit to the collection vessel. The accessory piercing member may contain needles, in some cases hollow needles, whose tips face the membrane. The accessory piercing member is configured such that when the buffer reservoir is in the first position relative to the collection vessel, the needles of the accessory piercing membrane stay clear off the membrane, and when the buffer reservoir is in the second position relative to the collection vessel, the accessory piercing member is pressed by another component of the sample collection unit so as to allow the needles to pierce the membrane, thereby bringing about the fluid communication as described above. In some embodiments, the another component of the sample collection unit may be the piercing member as described above.

In some embodiments, the sample collection unit may include a cap. In some embodiments, the cap may be manually or automatically fastened against the sample collection unit. In some embodiments, the cap may be fastened via a screw, a snap fit, adhesion, or any other fastening unit (s) . In some embodiments, the cap may merely be fastened by pressing it against the sample collection unit. In some embodiments, the fastening of the cap against the sample collection unit may bring the buffer reservoir from the first position to the second position relative to the collection vessel as mentioned above.

In some embodiments, the buffer reservoir may be integral to the cap, and when the cap is fastened against the sample collection unit, the buffer reservoir is brought into contact with the piercing member which allows the piercing member to pierce the membrane on the buffer reservoir to provide a fluid communication between the buffer reservoir and the collection vessel such that the content of the buffer reservoir flows from the buffer reservoir to the collection vessel.

In some embodiments, the collection vessel may have a blood collection member deposited within it. The blood collection member may be any blood collection member suitable for collection of blood. In some embodiments, the blood collection members comprise a finger prick.

In some embodiments, The buffer reservoir may comprise a membrane such that when the buffer reservoir is in a first position relative to the collection vessel, the membrane stays clear off the finger prick of the blood collection member, and when the buffer reservoir is in a second position relative to the collection vessel, the finger prick pierces the membrane to provide fluid communication between the buffer reservoir and the blood collection member such that the content of the buffer reservoir flows from the buffer reservoir to the blood collection member or the collection vessel.

Alternatively or additionally, the buffer reservoir may further comprise an accessory piercing member deposited in it such that when the buffer reservoir is in a first position relative to the collection vessel, the membrane stays clear off the accessory piercing member, and when the buffer reservoir is in a second position relative to the collection vessel, the accessory piercing member pierces the membrane to provide a fluid communication between the buffer reservoir and the blood collection member such that the content of the buffer reservoir flows from the buffer reservoir to the blood collection member or the collection vessel. In some embodiments, the accessory piercing member is configured to be proximal to the bottom of the collection vessel as compared to the membrane when the buffer reservoir is fit to the collection vessel. The accessory piercing member may contain needles, in some cases hollow needles, whose tips face the membrane. The accessory piercing member is configured such that when the buffer reservoir is in the first position relative to the collection vessel, the needles of the accessory piercing membrane stay clear off the membrane, and when the buffer reservoir is in the second position relative to the collection vessel, the accessory piercing member is pressed by another component of the sample collection unit so as to allow the needles to pierce the membrane, thereby bringing about the fluid communication as described above. In some embodiments, the another component of the sample collection unit may be the covering member of the blood collection member.

In some embodiments, the sample collection unit comprises a swab collection member. The swab collection member may be of any structure or unit that can be used for swab collection. The swab collection unit may include a collection surface and a support surface. The collection surface may be suitable for collecting a biological sample. The collection surface may include one or more reagents for sample preservation and/or processing.

In some embodiments, the swab collection member may be a cap having a channel extending therethrough to permit said at least one swab to be deposited in said collection vessel. The channel may be closable upon rotation of the cap. The swab collection member may have at least one cutting member that severs a longitudinal portion of a stem of the swab extending through said channel upon rotation of the cap. The collection vessel and/or the cap may be dimensioned such that upon depositing the swab in the collection vessel, the stem of the swab extends through the channel. Upon rotation of the cap, the cutting member may sever a longitudinal portion of the stem of the swab extending through said channel to provide the swab sealed in the collection vessel.

In some embodiments, the swab collection member may cover and/or secure the head of the swab, with the stem of the swab protruding away from the swab collection member. The swab collection member and the collection vessel may be fastened via a fastening unit (s) such that the swab collection member is encompassed in the collection vessel and relative movement is not allowed between the swab collection member and the collection vessel along the axis of the stem of the swab. Non-limiting fastening units suitable for this purpose include a snap fit, a screw connection, a quick release skewer, a pressure sensitive adhesive and the like. In some embodiments, the swab collection member may be rotated relative to the collection vessel along the axis of the stem of the swab such that the swab collection member and the collection vessel may be fastened. The fastening unit (s) may be integral to the swab collection member. The fastening unit (s) may be integral to the collection vessel. Alternatively or additionally, the fastening unit (s) may have two components, one integral to the collection vessel and one integral to the collection vessel, and the engagement of the two components of the fastening unit (s) may bring about the fastening between the swab collection member and the collection vessel.

After the swab collection member and the collection vessel are fastened, the head of the swab may be secured in the swab collection member. Alternatively, the head of the swab may be secured in the swab collection member prior to the fastening between the swab collection member and the collection vessel. While the head of the swab is secured in the swab collection member and the swab collection is encompassed in the collection vessel, the stem of the swab may be pulled away from the swab collection member, resulting in the separation between the head and the stem of the swab. The head may remain in the swab collection member. Optionally, the head may then be transferred into the collection vessel. Alternatively, the head may remain in the swab collection member which remains fastened to and encompassed in the collection vessel.

In some embodiments, the swab collection may comprise a piercing member deposited within it as described elsewhere herein. The piercing member within the swab collection may allow the buffer reservoir as described elsewhere herein to be pierced upon fastening of a cap as described elsewhere herein against the collection vessel to bring about the mixing of the content of the buffer reservoir with the swab.

In some embodiments, the swab collection member may be a securing/piercing element that can both secure the head of the swab during swab collection and later pierces the buffer reservoir as described elsewhere herein.

Dispensing Unit

In another aspect, the present disclosure provides a dispensing unit that directs dispensing of (i) a sample collection unit as described elsewhere herein, and/or (ii) one or more reagents as described elsewhere herein. In some embodiments, the dispensing unit, in some cases autonomously, directs dispensing of the sample collection unit and/or the one or more reagents upon authentication of a subject from which the sample is to be collected.

Alternatively or additionally, the dispensing unit may dispense any commodity that can be legally purchased by the user. Non-limiting examples of the commodities include over-the-counter drugs, prescription drugs, self-diagnostic kits, sample collection devices, dietary supplements, and the like.

In another aspect, the present disclosure provides a dispensing unit that dispenses a kit as described elsewhere herein, based on selection. The dispensing unit may, in some cases autonomously, dispenses a kit as described elsewhere herein, based on selection provided by a user. The selection may correspond to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining a presence, absence or amount of at least one target analyte in a biological sample of a subject. In some cases, the user may directly select a kit such that the dispensing unit dispenses the kit accordingly. In some cases, the user may select an assay or a disease, and the system, in some cases, the one or more processors as described elsewhere herein determine the kit to be dispensed such that the dispensing unit dispenses the kit accordingly.

In another aspect, the present disclosure provides a dispensing unit operatively coupled to the one or more computer processors as described elsewhere herein. The dispensing unit may, upon authentication of a subject, autonomously directs dispensing of (i) a sample collection unit as described elsewhere herein, and/or (ii) one or more reagents as described elsewhere herein.

In some embodiments, the dispensing unit may include a plurality of kits as described elsewhere herein. Each of the plurality of kits is directed to a given target assay among a plurality of target assays as described elsewhere herein.

In some embodiments, the dispensing unit may include an opening to permit dispensing of any commodities to be dispensed. In some embodiments, the dispensing unit may include an opening to permit dispensing of the kit based on selection. The opening may be a dispensing port through which any commodities or kits as described elsewhere herein can be dispensed. The dispensing port may have a shutter that can be deployed in at least two positions including an open position and a closed position.

In some embodiments, the dispensing unit may be directly coupled to an electronic device as described elsewhere herein. Alternatively, the dispensing unit may be remotely coupled to the electronic device. In one embodiment, the dispensing unit may be operatively coupled to the electronic device over a network. In some embodiments, the electronic device may provide selection to the dispensing unit.

In some embodiments, the dispensing unit may be operatively coupled to an electronic device as described elsewhere herein. The electronic device may provide the selection to the dispensing unit. The selection may be directed from the electronic device to the dispensing unit.

In some embodiments, the dispensing unit may have a footprint less than or equal to 100 feet². In some embodiments, the dispensing unit may have a footprint less than or equal to 95 feet², 90 feet², 85 feet², 80 feet², 75 feet², 70 feet², 65 feet², 60 feet², 55 feet², 50 feet², 45 feet², 40 feet², 35 feet², 30 feet², 25 feet², 20 feet², 19 feet², 18 feet², 17 feet², 16 feet², 15 feet², 14 feet², 13 feet², 12 feet², 11 feet², or 10 feet². In some embodiments, the footprint is less than or equal to 25 feet². In some embodiments, the footprint is less than or equal to 9 feet², 8 feet², 7 feet², 6 feet², 5 feet², 4 feet², 3 feet², 2 feet², or 1 feet².

In some embodiments, the dispensing unit may be within 5 feet of an electronic device as described elsewhere herein. In some embodiments, the dispensing unit may be within about 30 feet, 15 feet, 10 feet, 5 feet, 4 feet, 3 feet, 2 feet, 1 foot, 0.5 feet, 0.1 feet or directly adjacent to the electronic device.

In some embodiments, the dispensing unit may be attached to the electronic device. The dispensing unit may be directly attached to the electronic device. As another example, the dispensing unit is indirectly attached to the electronic device or not attached to the electronic device.

In some embodiments, the dispensing unit may be operatively coupled to the electronic device through a communication interface as described elsewhere herein. The dispensing unit may be operatively coupled to the electronic device wirelessly or through one or more wired interfaces. The dispensing unit may be operatively coupled to the electronic device through a network, such as the Internet or intranet.

In some embodiments, the dispensing unit may be brought in communication with one or more computer processors via a communication interface as described elsewhere herein. The communication may be any communication as described elsewhere herein. The communication may be local or remote communication. For example, the communication may be via a communication bus, such as a motherboard. Alternatively, the communication may be via a network, such as the Internet, an internet , an extranet, an intranet, a peer-to-peer network, a telecommunication network, and/or a data network.

In some embodiments, the dispensing unit may be operatively coupled to a sample processing unit as described elsewhere herein. The dispensing unit may be operatively coupled to the sample processing unit wirelessly or through one or more wired interfaces. The dispensing unit may be operatively coupled to the sample processing unit through a network, such as the Internet or intranet.

In some embodiments, the dispensing unit may be in a housing. In some embodiments, the dispensing unit may be in a housing together with the sample processing unit. Alternatively, the dispensing unit may be in a separate housing from the sample processing unit. The housing may be made of any suitable material. For example, the housing may be a metal housing, a plastic housing, a polymer housing, or the like.

In some embodiments, the dispensing unit may be within 5 feet of the sample processing unit. In some embodiments, the dispensing unit may be about 30 feet, 15 feet, 10 feet, 5 feet, 4 feet, 3 feet, 2 feet, 1 foot, 0.5 feet, 0.1 feet or directly adjacent to the sample processing unit.

In some embodiments, the dispensing unit may be attached to the sample processing unit. The dispensing unit may be directly attached to the sample processing unit. As another example, the dispensing unit is indirectly attached to the sample processing unit or not attached to the sample processing unit.

In some embodiments, communication may be established between the dispensing unit and an electronic device as described elsewhere herein. The dispensing unit maybe used to direct dispensing of (i) a sample collection unit as described elsewhere herein, and/or (ii) one or more reagents as described elsewhere herein.

Any commodities to be dispensed by the dispensing unit, including but not limited to the sample collection unit, one or more reagent, as well as over-the-counter drugs, prescription drugs, self-diagnostic kits, sample collection devices, dietary supplements, and the like as described elsewhere herein, may be displayed in a window through which the user may preview before making a selection. Alternatively or additionally, the aforesaid commodities may be previewed in a user interface as described elsewhere herein for the user to preview before making a selection.

In some embodiments, the dispensing unit may comprise a commodity transport unit to bring a commodity to be dispensed from a first area where the commodity is stored to a second area where the commodity is about to be dispensed to the user. In some embodiments, the commodity transport unit may be a rotating arm or a swinging arm. In some embodiments, the commodity transport unit may be a mandrill. The commodity transport unit may capture and/or release the commodity to be dispensed from and into the first area and/or the second area. In some embodiments, the dispensing unit may comprise a commodity pushout unit to push the commodity through the opening of the dispensing unit for the user to pick up after the commodity is in the second area. After the user picks up the dispensed commodity, the commodity pushout unit may retract into the dispensing unit through the opening. In some embodiments, the commodity pushout unit is a mandrill. The mandrill as described herein may be a rod capable of capturing the commodity on one end. The mandrill may be actuated to move along its longitudinal axis to transport the captured commodity. Once the mandrill brings the captured commodity to a desirable location, it may release the commodity to finish the transport.

In some embodiments, the commodity transport unit may bring commodity to be dispensed from a first area where the commodity is stored to a third area. The user may directly pick up the commodity. In some embodiments, the commodity transport unit may be a rotating arm or a swinging arm. In some embodiments, the commodity transport unit may be a mandrill. The mandrill may be a rod capable of capturing the commodity on one end. The mandrill may be actuated to move along its longitudinal axis to transport the captured commodity. Once the mandrill brings the captured commodity to a desirable location, it may release the commodity to finish the transport. The commodity transport unit may capture and/or release the commodity to be dispensed from and into the first area and/or the third area. In some embodiments, the third area is adjacent to the opening of the dispensing unit. After the commodity is transferred to the third area, the user may pick up the commodity through the opening of the dispensing unit. Alternatively, the opening may be shut off usually, but after the commodity is transferred to the third area, the opening may be opened to allow the user to pick up the commodity through it.

In some embodiments, the commodities are stored in a fridge or freezer before dispensing. The fridge or freezer maintains a temperature lower than the room temperature which is optimal for preservation of the commodities. The temperature of the fridge or freezer may be below 10℃, below 5℃, below 4℃, below 3℃, below 2℃, below 1℃, below 0℃, below -1℃, below -2℃, below -3℃, below -4℃, below -5℃, below -6℃, below -7℃, below -8℃, below -9℃, below -10℃, below -15℃, below -20℃, below -25℃, below -30℃, below -35℃, below -40℃, below -45℃, below -50℃, below -60℃, below -70℃, below -80℃, below -90℃, or even lower, or can be any temperature between those enumerated above.

Fig. 10 is a schematic diagram illustrating the layout of the front panel of the dispensing unit according to one embodiment of the present disclosure. The dispensing unit 1003 comprises an optional commodity display window 1031 and a commodity dispensing port 1032. The commodities to be dispensed are placed inside the dispensing unit such that the user may view the commodities via the commodity display window 1031. After authentication of user identity and user selection of assay at the user interface, one or more computer processors within the system determine the appropriate commodity to be dispensed to the user, and, optionally upon successful payment by the user, causes the dispensing unit to release the commodity to the commodity dispensing port 1032 for the user to pick up.

Sample Processing Unit

In another aspect, the present disclosure provides a sample processing unit that (1) receives a biological sample of a subject, and (2) processes the biological sample based on at least one target assay to determine the presence, absence or amount of at least one target analyte in the biological sample of the subject as described elsewhere herein. In some cases, the biological sample is collected of a subject. In some cases, the biological sample is collected using a kit as described elsewhere herein. In some cases, the biological sample is processed based on selection inputted by a user corresponding to at least one target assay from a plurality of target assays.

In some embodiments, the sample processing unit may be operatively coupled to a communication interface as described elsewhere herein. The sample processing unit may be operatively coupled to the communication interface wirelessly or through one or more wired interfaces. The sample processing unit may be operatively coupled to the communication interface through a network, such as the Internet or intranet.

In some embodiments, the sample processing unit may comprise an actuator. The actuator may transfers a biological sample to or from one or more sample processing stations of the sample processing unit. In some embodiments, the actuator may be a robotic arm.

In some embodiments, the sample processing unit may receive a biological sample in a sample collection unit as described elsewhere herein. The sample collection unit may be a sample collection unit for collecting a solid biological sample, a liquid biological sample, a blood sample, a swab sample or other type of biological samples.

In some embodiments, the sample processing unit may include an opening to permit a user to deposit a biological sample. The user may deposit the biological sample via a sample receiving port as described elsewhere herein. The sample receiving port may have a shutter that can be deployed in at least two positions including an open position and a closed position. After deposited by user to the sample processing unit, the biological sample may be transferred to a storage element within the sample processing unit as described elsewhere herein, prior to being assayed or transported.

In some embodiments, the sample processing unit may be directly coupled to an electronic device as described elsewhere herein. Alternatively, the sample processing unit may be remotely coupled to the electronic device. In one embodiment, the sample processing unit may be operatively coupled to the electronic device over a network.

Alternatively, the sample processing unit may be remotely coupled to the electronic device. In one embodiment, the sample processing unit may be operatively coupled to the electronic device over a network. In one embodiment, the sample processing unit may be operatively coupled to the electronic device via a communication interface as described elsewhere herein.

In some embodiments, the sample processing unit may have a footprint less than or equal to 100 feet². In some embodiments, the sample processing unit may have a footprint less than or equal to 95 feet², 90 feet², 85 feet², 80 feet², 75 feet², 70 feet², 65 feet², 60 feet², 55 feet², 50 feet², 45 feet², 40 feet², 35 feet², 30 feet², 25 feet², 20 feet², 19 feet², 18 feet², 17 feet², 16 feet², 15 feet², 14 feet², 13 feet², 12 feet², 11 feet², or 10 feet². In some embodiments, the footprint is less than or equal to 25 feet². In some embodiments, the footprint is less than or equal to 9 feet², 8 feet², 7 feet², 6 feet², 5 feet², 4 feet², 3 feet², 2 feet², or 1 feet².

In some embodiments, the sample processing unit may be within 5 feet of an electronic device as described elsewhere herein. In some embodiments, the dispensing unit may be within about 30 feet, 15 feet, 10 feet, 5 feet, 4 feet, 3 feet, 2 feet, 1 foot, 0.5 feet, 0.1 feet or directly adjacent to the electronic device.

In some embodiments, the sample processing unit may be attached to the electronic device. The sample processing unit may be directly attached to the electronic device. As another example, the sample processing unit is indirectly attached to the electronic device or not attached to the electronic device.

In some embodiments, the sample processing unit may authenticate a subject as described elsewhere herein. For example, the sample processing unit may authenticate the subject by any suitable authentication approach, including but not limited to fingerprint, biometric identification, biometric card, PIN with/without a user name, barcode or two-dimensional code, and the like.

In some embodiments, the sample processing unit may be operatively coupled to a dispensing unit as described elsewhere herein. The sample processing unit may be operatively coupled to the dispensing unit wirelessly or through one or more wired interfaces. The sample processing unit may be operatively coupled to the dispensing unit through a network, such as the Internet or intranet.

In some embodiments, the sample processing unit may be in a housing. In some embodiments, the sample processing unit may be in a housing together with the dispensing unit. Alternatively, the sample processing unit may be in a separate housing from the dispensing unit. The housing may be made of any suitable material. For example, the housing may be a metal housing, a plastic housing, a polymer housing, or the like.

In some embodiments, the sample processing unit may be within 5 feet of the dispensing unit. In some embodiments, the sample processing unit may be about 30 feet, 15 feet, 10 feet, 5 feet, 4 feet, 3 feet, 2 feet, 1 foot, 0.5 feet, 0.1 feet or directly adjacent to the dispensing unit.

In some embodiments, the sample processing unit may be attached to the dispensing unit. The sample processing unit may be directly attached to the dispensing unit. As another example, the sample processing unit is indirectly attached to the dispensing unit or not attached to the dispensing unit.

In some embodiments, communication may be established between the sample processing unit and an electronic device as described elsewhere herein. The communication may be any communication as described elsewhere herein. The communication may be local or remote communication. For example, the communication may be via a communication bus, such as a motherboard. Alternatively, the communication may be via a network, such as the Internet, an internet , an extranet, an intranet, a peer-to-peer network, a telecommunication network, and/or a data network.

The sample processing unit may comprise several sample processing stations for carrying out various sample processing steps. Non-limiting sample processing steps include sample preservation, sample preparation, assay, authentication, detection, and the like.

The sample processing unit may comprise one or more sample preservation units for preserving the collected sample that it receives. The sample preservation unit (s) enables the collected sample to retain its biological properties and activities during storage and/or transport for the target assay, or recover its original biological properties and activities later for the target assay. The sample preservation unit (s) may employ one or more of the following preservation techniques: freezing, fridging, lyophilization, glassification, sol gel, and other suitable techniques for preserving samples.

The sample processing unit may comprise one or more sample preparation units for preparing the collected sample for the target assay. Depending on the target assay, various sample preparation steps may be employed as appropriate. Non-limiting examples of the various sample preparation steps that may be suitable to the system/method of the present disclosure include lysis, centrifuge, separation, immobilization, pretreatment, conjugation, and any other suitable steps for the purpose of the present disclosure.

For example, the sample preparation unit (s) may lyse the collected sample in a lysis step. Lysis of cells such as bacteria, or host cells, or lysis of particles or viruses may facilitate the target assay by freeing target molecules from cellular or other compartment. Various lytic techniques may be employed. Non-limiting examples of lytic techniques that may be suitable to the system/method of the present disclosure include mechanical lysis, electrochemical lysis, chemical lysis, acoustic lysis, thermal lysis, electrical lysis, and any other suitable lytic techniques for the purpose of the present disclosure.

For example, the sample preparation unit (s) may separate the collected sample into its individual components in a separation step. Separation may be desirable to avoid interference from unwanted components of the sample. Various separation techniques may be employed. Non-limiting examples of separation techniques that may be suitable to the system/method of the present disclosure include electrophoresis, centrifuge, fractionation, microfluidic separation, chromatography, and any other suitable lytic techniques for the purpose of the present disclosure.

For example, the sample preparation unit (s) may pretreat the sample in a pretreatment step. Pretreatment may be desirable to subject the collected sample to appropriate environment for the target assay. Pretreatment may involve heating, cooling, shaking, sonication, mixture with appropriate reagents, and or any other suitable pretreatment in the context of the target assay.

In some embodiments, the collected sample is directly preserved or subject to the target assay without preparation.

The sample processing unit may comprise one or more assay units for conducting any target assay as described elsewhere herein. For example, the sample processing unit may comprise one or more units for conducting the following target assays: nucleic acid amplification, sequencing, immunoassays, gel electrophoresis, chemiluminescent assays, fluorescent assays, blot assays, and any other suitable target assays for the purpose of the present disclosure.

In some embodiments, the sample processing unit comprises a nucleic acid amplification unit for conducting nucleic acid amplification as described elsewhere herein. The nucleic acid amplification unit for conducting nucleic acid amplification may be a thermocycler. In some embodiments, the sample processing unit comprises a sequencing unit for conducting sequencing as described elsewhere herein. The sequencing unit for conducting sequencing may be a sequencing platform as described elsewhere herein.

The sample processing unit may comprise a sample receiving element for receiving a biological sample in a sample collection unit as described elsewhere herein. The sample receiving element may comprise a sample receiving port. The sample receiving port may have a shutter that can be deployed in at least two positions including an open position and a closed position. The shutter may usually be deployed in the closed position which prevents the access to the sample receiving port. The shutter may be deployed in the open position to allow access to the sample receiving port upon a user input via the user interface.

Optionally, the sample receiving element may further comprise a barcode/two-dimensional code scanner for scanning a barcode/two-dimensional code on the sample collection unit. A user input may be presented by placing the sample collection unit in proximity to the barcode/two-dimensional code scanner such that a barcode/two-dimensional code on the sample collection unit that contains information can be scanned by the code scanner. Such information may be information regarding the identity of the subject from which the sample was collected, the type of sample collected, and/or the target assay. Upon scanning of the barcode/two-dimensional code, the information contained on the code is extracted and processed by a processor to determine whether the sample collection unit can be recovered. The processor may be the computer processor as described elsewhere herein or a separate processor.

If the processor determines that the sample in question can be recovered, it causes the shutter to be deployed in the open position to allow the user to place the sample collection unit inside the sample receiving port. Once the sample collection unit is placed inside the sample receiving port, the sample receiving element may cause the sample collection unit to be transported into a storage position inside the sample processing unit, or a separate storage unit. For example, the sample collection unit may be transported into the storage position by the action of a mandrill and/or a rotating arm. Conversely, if the processor determines that the sample in question cannot be recovered, it causes the shutter to remain to be deployed in the open position to prevent the user from placing the sample collection unit inside the sample receiving port. Additionally, the processor may be programmed to automatically cause the shutter to be deployed in the closed position after the shutter has been deployed in the open position for a period of time, no matter whether anything has been placed inside the sample receiving port. The period of time may be 5 to 10 seconds or any period of time falls within the aforesaid range.

In some embodiments, the received sample is transferred to a fridge or a freezer, for example, by the action of a mandrill and/or a rotating arm. The fridge or freezer maintains a temperature lower than the room temperature which is optimal for preservation of the sample. The temperature of the fridge or freezer may be below 10℃, below 5℃, below 4℃, below 3℃, below 2℃, below 1℃, below 0℃, below -1℃, below -2℃, below -3℃, below -4℃, below -5℃, below -6℃, below -7℃, below -8℃, below -9℃, below -10℃, below -15℃, below -20℃, below -25℃, below -30℃, below -35℃, below -40℃, below -45℃, below -50℃, below -60℃, below -70℃, below -80℃, below -90℃, or even lower, or can be any temperature between those enumerated above. In some embodiments, the received sample is stored in a different fridge or freezer than where the commodity to be dispensed is stored. In some embodiments, the received sample is stored in the same fridge or freezer as where the commodity to be dispensed is stored. In the latter circumstance, the received sample is placed in a separate region from where the commodity to be dispensed is stored in the fridge or freezer to prevent it from being improperly dispensed.

Fig. 11 is a schematic diagram illustrating the layout of the front panel of a housing comprising both the dispensing unit and the sample processing unit according to an embodiment of the present disclosure. In Fig. 11, the dispensing unit/sample processing unit 1003/1004 further comprises a sample receiving element 1041 for recovering the sample collected by the user. In some embodiment, the commodity is a sample collection device. After the user collects sample in the sample collection device, the user may put the sample collection device with collected sample back into the dispensing unit/sample processing unit 1003/1004 via the sample receiving element 1041.

Fig. 12 is a schematic diagram of a sample receiving element according to an embodiment of the present disclosure. The sample receiving element 1041 comprises a barcode/two-dimensional code scanner 1041a and a sample receiving port 1041b. The sample receiving port 1041b may have a shutter that can be deployed in an open position and a closed position to allow or deny the access to the sample receiving port 1041b. The shutter may be deployed in the open position to allow access to the sample receiving port 1041b upon a user input. The user input may be presented by placing the commodity in proximity to the barcode/two-dimensional code scanner 1041a such that a barcode/two-dimensional code on the commodity that contains information on the commodity can be scanned by the code scanner 1041a. Upon scanning of the barcode/two-dimensional code, the information contained on the code is extracted and processed by a computer processor to determine whether the commodity can be recovered.

Authentication Unit

In another aspect, the present disclosure provides an authentication unit that authenticates a user. The authentication unit may allow determination of the identity of the user and/or subject in various manners. In some embodiments, the user interface prompts the user to verify his/her identity. The user interface may comprise a graphical element which includes a message to the user prompting selection of an authentication option. The user interface may further comprise one or more graphical elements describing various authentication options.

Non-limiting options for authentication of identity may include fingerprint, biometric identification, biometric card, PIN with/without a user name, barcode or two-dimensional code, and the like. Accordingly, the authentication unit may comprise one or more of the following components: a card reader, a biometric scanner, and a barcode/two-dimensional code scanner.

In some embodiment, the authentication unit comprises a biometric scanner. The biometric scanner reads biometric traits of the user for authentication. Non-limiting examples of biometric traits may include fingerprint, palm veins, face recognition, DNA, palm print, hand geometry, iris recognition, retina and odor/scent. In some embodiments, the authentication unit may be a fingerprint scanner or a retina scanner. In some embodiments, the biometric trait is a finger print and the biometric scanner is a fingerprint scanner. The fingerprint scanner may be any available fingerprint scanner, including those that recognize fingerprints by optical recognition, ultrasound recognition, or active or passive capacitance.

In some embodiments, the authentication unit may measure a characteristic of the subject. For example, the characteristic may be a temperature, resistance, impedance, capacitance, luminescence, fluorescence of the subject. In some embodiments, the authentication unit may be a impedance scanner.

In some embodiments, the authentication unit may be part of an electronic device as described elsewhere herein. In some embodiments, the authentication unit may be integral to the electronic device. In some embodiments, the authentication unit may be attached to the electronic device. The authentication unit may be directly attached to the electronic device. As another example, the authentication unit is indirectly attached to the electronic device or not attached to the electronic device.

In some embodiments, the authentication unit may be part of a system as described elsewhere herein. In some embodiments, the authentication unit may be integral to the system. In some embodiments, the authentication unit may be attached to the system. The authentication unit may be directly attached to the system. As another example, the authentication unit is indirectly attached to the system or not attached to the system.

In some embodiments, the authentication unit may be operatively coupled to one or more computer processors as described elsewhere herein. The authentication unit may be operatively coupled to the one or more computer processors wirelessly or through one or more wired interfaces. The authentication unit may be operatively coupled to the one or more computer processors through a network, such as the Internet or intranet.

In some embodiments, the authentication unit may comprise a card reader. The card reader may comprise a card insert. The card insert may accommodate a swipe card and/or a smart card. In some cases, the card reader comprises both a card insert for swipe cards and a card insert for contact smart cards. A “swipe card” stores information in a magnetic stripe. A “contact smart card” stores information in an embedded integrated circuit. Both of them need to be inserted into the card insert to allow information to be extracted. The swipe card and/or the contact smart card may be a credit card, a debit card, a customary identification card, or any other card that allows authentication to be made upon.

In some embodiments, the card reader may comprise a contactless card reader. The contactless card reader allows information to be extracted from a card (aproximity card, a contactless card, or a contactless smart card) by placing the card close to the card reader, without inserting the card into a card insert. The contactless card reader may use RFID (radio frequency identification) technique to extract information from the card. The card may be a credit card, a debit card, a customary card, or any other card that allows authentication to be made upon. Alternatively or additionally, the contactless card reader may extract information from a smartphone with integrated RFID device such that authentication may be carried out. For example, the user may use a smartphone app that utilizes the RFID technique to communicate with the contactless card reader for authentication.

In some embodiment, the authentication comprises a barcode/two-dimensional code scanner. The barcode/two-dimensional code scanner may scan a barcode or a two-dimensional code provided by the user to extract information. The information may be information on the identity of the user. For example, the user may use a smartphone app to generate a barcode or two-dimensional code with identity information which can be read by the barcode/two-dimensional code scanner to carry out the authentication. In some embodiments, the barcode/two-dimensional code may be printed on an access card held by the user to provide personal identity of the user. In some embodiments, the barcode/two-dimensional code may be printed on a wristband of the user to provide personal identity of the user. Alternatively, the barcode/two-dimensional code may be printed on other items held by the user. The user may scan the barcode/two-dimensional on the card, wristband, or other items with the barcode/two-dimensional code scanner for authentication.

In some embodiments, the authentication unit may comprise a video and/or audio device. The video and/or audio recording device may be activated to record the image and/or voice of the user upon operation of the system/method as described herein. The recorded image and/or voice may be stored in one or more storage devices which are a part of the system. The stored image and/or voice may be retrieved later for verification of the identity of the user. Alternatively or additionally, the video and/or audio device transmits the image and/or voice of the user in real-time over a network to a distal authenticator for authentication. The authenticator may be a human or an authentication device. The distal authenticator may provide instant authentication to the user based on the transmitted image and/or voice.

Payment Unit

In another aspect, the present disclosure provides a payment unit that allows payment from the user. Non-limiting options for making the payment may include cash, credit card, debit card, pre-paid card, token, smart card, smart phone (Alipay, Wechat pay, apple pay, etc. ) , and the like. Accordingly, the payment unit may comprise one or more of the following components: a cash acceptor and dispenser, a card reader, a biometric scanner, and/or a barcode/two-dimensional code scanner.

In some embodiments, the system dispenses a commodity after authentication and payment are made. In some embodiments, the system dispenses a commodity after authentication and payment matches each other. In some embodiments, when payment does not go through, the user interface of the system displays an error message.

In some embodiments, the authentication is performed prior to payment. In some embodiments, the authentication is performed following payment. In some embodiments, the authentication is performed simultaneously with payment. In some embodiments, the authentication unit as described elsewhere herein is also the payment unit.

In some embodiments, the user interface prompts the user for payment. The user interface may comprise a graphical element which includes a message to the user prompting selection of a payment option. The user interface may further comprise one or more graphical elements describing various payment options.

In some embodiments, the payment unit comprises a cash acceptor and dispenser. The cash acceptor and dispenser can accept cash inserted by the user and dispense a change, if applicable. Accordingly, the cash acceptor and dispenser may comprise a cash insert slot for the user to insert cash. The cash acceptor and dispenser may further comprise a port for the change to be dispensed. The cash acceptor and dispenser may further comprise a token slot through which coins or token may be inserted. A person skilled in the art understands that a pre-paid token may be inserted into the token slot for payment in place of cash.

In some embodiments, the payment unit comprises a card reader. The card reader may comprise a card insert. The card insert may accommodate a swipe card and/or a smart card. In some cases, the card reader comprises both a card insert for swipe cards and a card insert for contact smart cards. A “swipe card” stores information in a magnetic stripe. A “contact smart card” stores information in an embedded integrated circuit. Both of them need to be inserted into the card insert to allow information to be extracted. The swipe card and/or the contact smart card may be a credit card, a debit card, a pre-paid card, or any other card that allows payment to be made upon.

In some embodiments, the card reader may comprise a contactless card reader. The contactless card reader allows information to be extracted from a card (aproximity card, a contactless card, or a contactless smart card) by placing the card close to the card reader, without inserting the card into a card insert. The contactless card reader may use RFID (radio frequency identification) technique to extract information from the card. The card may be a credit card, a debit card, a pre-paid card, or any other card that allows payment to be made upon. Alternatively, the card may be an identification card which can be used to verify the identity of the user. Alternatively or additionally, the contactless card reader may extract information from a smartphone with integrated RFID device such that payment may be carried out. For example, the user may use a smartphone payment service that utilizes the RFID technique (e.g., Apple Pay) to communicate with the contactless card reader to make the payment.

In some embodiment, the payment unit comprises a biometric scanner. The biometric scanner reads biometric traits of the user. As mentioned above, the biometric scanner may be used for authentication purpose. In some embodiments, the biometric scanner may also be used to allow payment through authentication of the user. For example, the user may have credit in the system which he/she may redeem by authentication via the biometric scanner. Non-limiting examples of biometric traits may include fingerprint, palm veins, face recognition, DNA, palm print, hand geometry, iris recognition, retina and odor/scent. In some embodiments, the biometric trait is a finger print and the biometric scanner is a fingerprint scanner. The fingerprint scanner may be any available fingerprint scanner, including those that recognize fingerprints by optical recognition, ultrasound recognition, or active or passive capacitance.

In some embodiment, the payment unit comprises a barcode/two-dimensional code scanner. The barcode/two-dimensional code scanner may scan a barcode or a two-dimensional code provided by the user to extract information. The information may be payment information. For example, the user may use a smartphone payment service (e.g., Alipay, Wechat Pay) to generate a barcode or two-dimensional code with payment information which can be read by the barcode/two-dimensional code scanner to carry out the payment.

In some embodiments, if the information obtained by the authentication unit in the authentication step matches the information obtained by the payment unit in the payment step, the system proceeds to dispense a commodity. If the information obtained by the authentication unit in the authentication step does not match the information obtained by the payment unit in the payment step, the user interface may display an error message and prompt the user to start over.

Fig. 9 is a schematic diagram of a payment/authentication module. It is envisioned that a plurality of elements may be encompassed in the payment/authentication module 915, including a cash acceptor and dispenser 9151, a card reader 9152, a biometric scanner 9153, and/or a barcode/two-dimensional code scanner 9154. Each of these elements may be used for payment and/or identity authentication.

Computer Processor

In another aspect, the present disclosure provides a computer processor individually or collectively programmed to perform one or more processes as described elsewhere herein.

In some embodiments, the computer processor may be individually or collectively programmed to (a) receive a selection inputted by a user in a display of an electronic device as described elsewhere herein, and (b) direct dispensing of (i) a sample collection unit for collecting a biological sample of a subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the computer processor may be individually or collectively programmed to (1) monitor a quantity of a plurality of kits or a subset thereof, and (2) provide a notification when the quantity approaches or is below a threshold.

In some embodiments, the notification is directed over a network to a computer server that receives the notification. The network may be any suitable network. For example, the network may be the Internet, an internet , an extranet, an intranet, a peer-to-peer network, a telecommunication network, and/or a data network.

In some embodiments, the computer processor may be individually or collectively programmed to receive selection inputted by a user subsequent to the user being provided a characteristic as described elsewhere herein.

In some embodiments, the computer processor may be individually or collectively programmed to (a) receive selection inputted by a user in a user interface, and (b) transmit the selection to a dispensing unit that directs dispensing of (i) a sample collection unit for collecting a biological sample of a subject, and/or (ii) one or more reagents necessary for processing the biological sample of the subject based on the selection.

In some embodiments, the computer processor may be individually or collectively programmed to receive selection inputted by a user subsequent to the user being provided a characteristic of the subject as described elsewhere herein.

In some embodiments, the computer processors may be in communication with an authentication unit as described elsewhere herein. The communication may be any communication as described elsewhere herein. The communication may be local or remote communication. For example, the communication may be via a communication bus, such as a motherboard. Alternatively, the communication may be via a network, such as the Internet, an internet , an extranet, an intranet, a peer-to-peer network, a telecommunication network, and/or a data network.

In some embodiments, the computer processor may be operatively coupled to a communication interface as described elsewhere herein. The computer processor may be operatively coupled to the communication interface wirelessly or through one or more wired interfaces. The dispensing unit may be operatively coupled to the communication interface through a network, such as the Internet or intranet.

In some embodiments, the computer processor may be operatively coupled to a display screen as described elsewhere herein. The computer processor may be operatively coupled to the display screen wirelessly or through one or more wired interfaces. The dispensing unit may be operatively coupled to the display screen through a network, such as the Internet or intranet.

In some embodiments, the computer processor may be brought in communication with a dispensing unit by a communication interface as described elsewhere herein. The communication may be any communication as described elsewhere herein. The communication may be local or remote communication. For example, the communication may be via a communication bus, such as a motherboard. Alternatively, the communication may be via a network, such as the Internet, an internet , an extranet, an intranet, a peer-to-peer network, a telecommunication network, and/or a data network.

In some embodiments, information regarding the presence of and/or an amount of the target analyte (e.g., a biomarker, a nucleic acid, and/or a protein) can be outputted to a recipient. Information regarding the target analyte can be outputted via any suitable approach. Such information can be provided in real-time while the nucleic-acid amplification is underway. In other instances, the information can be provided once the target assay has been completed. In some instances, some data can be provided in real-time while other data can be presented once the amplification is completed.

In some embodiments, such information can be provided verbally to a recipient. In some embodiments, such information can be provided in a report. A report can include any number of desired elements, with non-limiting examples that include information regarding the subject (e.g., sex, age, race, health status, etc. ) , raw data, processed data (e.g. graphical displays (e.g., figures, charts, data tables, data summaries) , sequencing results, determined cycle threshold values for nucleic acid amplification, calculation of starting amount of target polynucleotide, conclusions about the presence of the target analyte, diagnosis information, prognosis information, disease information, and the like, and combinations thereof. The report can be provided as a printed report (e.g., a hard copy) or can be provided as an electronic report. In some embodiments, including cases where an electronic report is provided, such information can be outputted via an electronic display, such as a monitor or television, a screen operatively linked with a unit used to obtain the amplified product, a tablet computer screen, a mobile device screen, and the like. Both printed and electronic reports can be stored in files or in databases, respectively, such that they are accessible for comparison with future reports.

Moreover, a report can be transmitted to the recipient at a local or remote location using any suitable communication medium including, for example, a network connection, a wireless connection, or an internet connection. In some embodiments, a report can be sent to a recipient’s device, such as a personal computer, phone, tablet, or other device. The report can be viewed online, saved on the recipient’s device, or printed. A report can also be transmitted by any other suitable approach for transmitting information, with non-limiting examples that include mailing a hard-copy report for reception and/or for review by a recipient.

Moreover, such information can be outputted to various types of recipients. Non-limiting examples of such recipients include the subject from which the biological sample was obtained, a physician, a physician treating the subject, a clinical monitor for a clinical trial, a nurse, a researcher, a laboratory technician, a representative of a pharmaceutical company, a health care company, a biotechnology company, a hospital, a human aid organization, a health care manager, an electronic system (e.g., one or more computers and/or one or more computer servers storing, for example, a subject’s medical records) , a public health worker, other medical personnel, and other medical facilities.

Sensing Unit

In some aspect, the present disclosure provides a sensing unit that captures a characteristic of a subject.

In some embodiments, the characteristic may be a sound, image or video of the subject. If the characteristic is an image or a video, the sensing unit may be a camera, a digital camera, a video recorder, a camcorder, a smartphone or tablet computer having a camera or video recorder functionality, and the like, and/or the characteristic may be provided to the user by an electronic display such as a monitor, a television, a tablet computer screen, a mobile device screen, and the like. If the characteristic is a sound, the sensing unit may be a microphone, a smartphone or tablet computer having a microphone functionality, and the like, and/or the characteristic may be provided to the user via a speaker, a headphone, a blue tooth earphone, and the like.

In some embodiments, the characteristic may be a temperature, resistance, impedance, capacitance, luminescence, or fluorescence of the subject. Accordingly, the sensing unit may be an electrochemical sensor, an optical sensor, an electronic sensor, a piezoelectric sensor, a gravimetric sensor, a pyroelectric sensor, and the like, and/or the characteristic may be provided to the user as a report as described elsewhere herein, for example, provided to the user as a printed report or an electronic report, the latter could be via an electronic display such as a monitor, a television, a tablet computer screen, a mobile device screen, and the like

Quantification Methods

The subject methods can involve assessing relative or absolute quantity or concentration of at least one target analyte in the biological sample. In the context of the present disclosure, the quantity of the target analyte in the biological sample may be represented as the mass, the amount of substance, or the number of the target analyte. Accordingly, the concentration of a target analyte in the biological sample may be a mass concentration, a molar concentration, or a number concentration. If the biological sample is a fluid, the mass concentration, molar concentration or number concentration can be represented as the mass/amount of substance/number of the target analyte divided by the volume of the fluid. If the biological sample is a solid and is rendered a lysate, a suspension, an extract, or a homogenate during sample preparation, the volume of the lysate, suspension, extract, or homogenate thus produced may be used in place of the volume of the sample. In addition, if the target analyte is a bacterium or a fungus, the quantity of the target analyte may be measured in colony-forming units (cfu) . Accordingly, the concentration of the target analyte may be represented in cfu divided by the volume of the sample as defined herein, for example, in cfu/ml.

The quantity or the concentration of the target analyte may be normalized such that the quantity or the concentration of the target analyte may be comparable across different biological samples. The different biological samples may be biological samples collected from different subjects. The different biological samples may be biological samples collected from the same subject at different times. The different biological samples may be different aliquots of biological samples collected from the same subject. For example, the quantity or the concentration may be normalized by an internal standard. The internal standard may represent the quantity or the concentration of a relatively constant component of the biological sample. A component may be considered relatively constant if the quantity or the concentration of the component does not fluctuate across different biological samples under the conditions where the biological sample is collected (e.g. within 10％, 5％, 1％, or less of each other) . In some embodiments, the internal standard may be the quantity or concentration of another analyte.

The relative quantity of a target analyte in the biological sample may be represented as a ratio between the quantity of the target analyte and another reference quantity. In some embodiments, the reference quantity is the quantity of one or more subsets of or all target analytes in the biological sample. In some embodiments, the reference quantity is the quantity of one or more subsets of the target analytes. In some embodiments, the reference quantity is the quantity of all target analytes. In some embodiments, the reference quantity is the quantity of a specific target analyte. In some embodiments, the reference quantity for a target analyte is the quantity of another target analyte. In some embodiment, the reference quantity for a target analyte is the quantity of the same target analyte in a control biological sample. The control biological sample may be a biological sample collected from a healthy individual. The control biological sample may be a biological sample collected from the subject when the subject was healthy or appeared to be healthy. The control biological sample may be a biological sample collected from an individual with known health state. The known health state may be a diagnosis of a certain disease, disorder, or condition. The known health state may be a prognosis of a certain disease, disorder, or condition. The known health state may be the known health state of the subject himself/herself at a different time.

The relative concentration of a target analyte in the biological sample may be represented as a ratio between the concentration of the target analyte and another reference concentration. In some embodiments, the reference concentration is the concentration of one or more subsets of or all target analytes in the biological sample. In some embodiments, the reference concentration is the concentration of one or more subsets of target analytes. In some embodiments, the reference concentration is the concentration of all target analytes. In some embodiments, the reference concentration is the concentration of a specific target analyte.

In some embodiments, the presence, absence, quantity, or concentration of 1, 2, 3, 4, 5, 10, 15, 25, 50, 100, 500, 1000, 5000, or more target analytes are assessed.

In some embodiments, the presence, absence, relative quantity, or relative concentration of 1, 2, 3, 4, 5, 10, 15, 25, 50, 100, 500, 1000, 5000, or more analytes are detected over a certain period of time to determine the change of relative quantity or concentration of the target analytes over the period of time. In some embodiments, the period of time is about or at least 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, or more than 1 year.

Target Assay

In some aspect, the present disclosure provides one or more target assays directed to determining presence, absence or amount of at least one target analyte in a biological sample of a subject. The one or more target assays may include one, two, three, four, five, six, seven, eight, nine, ten, or more than ten target assays.

In some embodiments, the target assay may be directed to determining presence, absence or amount of at least one target analyte in a biological sample. The target assay may be any assay suitable for determining presence, absence, or amount of the at least one target analyte in the biological sample. The target assay may be a nucleic acid amplification assay, a sequencing assay, an immunoassay, an electrophoretic assay, an affinity assay, or any other assays suitable for the purpose of the present disclosure.

In some embodiments, the plurality of target assays may be directed to different target analytes. Alternatively, the plurality of target assays may be directed to the same target analyte. Furthermore, the plurality of target assays may be directed to more than one analytes, wherein the number of analytes is smaller than the number of the target assays. In some cases, at least two, three, four, five, or any number up to the total number of the plurality of target assays are directed to the same analyte.

In some embodiments, the plurality of target assays may be the same type of assay. In some cases, at least two, three, four, five, or any number up to the total number of the plurality of target assays may be the same type of assay.

In some embodiments, the target assays include array hybridization, nucleic acid sequencing or nucleic acid amplification.

In some embodiments, the at least one target assays may be an amplification protocol. In some embodiments, the target assay is a nucleic amplification assay. Non-limiting examples of nucleic acid amplification methods include reverse transcription (e.g., reverse transcription PCR (RT-PCR) , primer extension, polymerase chain reaction (PCR) , ligase chain reaction (LCR) , helicase-dependent amplification, asymmetric amplification, rolling circle amplification, and multiple displacement amplification (MDA) . In cases where a nucleic acid is deoxyribonucleic acid (DNA) is amplified, any DNA amplification method may be employed. Non-limiting examples of DNA amplification methods include polymerase chain reaction (PCR) , variants of PCR (e.g., real-time PCR, allele-specific PCR, assembly PCR, asymmetric PCR, digital PCR, emulsion PCR, dial-out PCR, helicase-dependent PCR, nested PCR, hot start PCR, inverse PCR, methylation-specific PCR, miniprimer PCR, multiplex PCR, nested PCR, overlap-extension PCR, thermal asymmetric interlaced PCR, touchdown PCR) , and ligase chain reaction (LCR) . In some cases, DNA amplification is linear. In some cases, DNA amplification is exponential. In some cases, DNA amplification is achieved with nested PCR, which can improve sensitivity of detecting amplified DNA products.

In some embodiments, the target assay is a sequencing assay. The sequencing assay may be any sequencing assay as described elsewhere herein. Non-limiting sequencing assay that may be suitable for the purpose of the present disclosure include Sanger sequencing, sequencing by synthesis, such as pyrosequencing, Illumina sequencing, sequencing by ligation such as polony sequencing and SOLiD sequencing, nanopore sequencing, semiconductor sequencing, and the like. Sequencing may be parallel or massively parallel sequencing. Sequencing may be single molecule sequencing. Sequencing may include nucleic acid amplification, such as polymerase chain reaction (PCR) or digital PCR. Sequencing may be targeted sequencing.

In some embodiment, the target assay is an immunoassay. The immunoassay may be any immunoassay suitable for the purpose of the present disclosure. Non-limiting immunoassay hat may be suitable for the purpose of the present disclosure include ELISA, ELISA, ELISPOT, Enzyme Multiplied Immunoassay Technique, RAST test, Radioimmunoassay, Radiobinding assay, Immunofluorescence, and the like.

Kits

In some aspect, the present disclosure provides kits for sample collection, processing and/or analysis. A kit may include a sample collection unit and/or one or more reagent as described elsewhere herein. The kit may be directed to a given target assay as described elsewhere herein. The kit may comprise (1) a sample collection unit for collecting a biological sample of a subject, and (2) one or more reagents necessary for processing the biological sample of the subject based on selection.

In some embodiments, the kit may be used to collect a biological sample from a subject. The sample collection unit may be a sample collection unit for solid samples, a sample collection unit for liquid samples, a sample collection unit for blood samples, a sample collection unit for swab samples, and the like.

In some embodiments, the kit may include a finger prick. The finger prick may be used by a user or the subject to prick a body surface (e.g., finger) of the subject to retrieve a tissue sample from the subject, such as a blood sample. Alternatively or additionally, the kit may include a swap.

In some embodiments, the kit may be among a plurality of kits. In some embodiments, the kit may be included in a dispensing unit as described elsewhere herein among a plurality of kits. Each of the plurality of kits may be directed to a given target assay among a plurality of target assays as described elsewhere herein.

In some embodiments, the quantity of the plurality of kits or a subset thereof may be monitored. Moreover, a notification may be provided when said quantity approaches or is below a threshold as described elsewhere herein.

In some embodiments, the kit may be dispensed, in some cases through an opening of the dispensing unit, based on selection as described elsewhere herein. The opening may be a dispensing port through which any kits as described elsewhere herein can be dispensed. The dispensing port may have a shutter that can be deployed in at least two positions including an open position and a closed position.

In some embodiments, the kit may further comprise instructions for collecting a biological sample from a subject. The instructions may be printed or stuck on the exterior of the kit. Alternatively, the instructions may be provided as separate printed material within the kit. In some cases, the instructions may be provided via a network to the user as described elsewhere herein. For example, the instructions may be provided via the Internet, an internet , an extranet, an intranet, a peer-to-peer network, a telecommunication network, and/or a data network to a user terminal as described elsewhere herein.

In some embodiments, the kit may be autonomously dispensed by a dispensing unit as described elsewhere herein, based on selection provided by a user. The selection may correspond to at least one target assay from a plurality of target assays. The at least one target assay may be directed to determining a presence, absence or amount of at least one target analyte in a biological sample of a subject.

In some embodiments, a biological sample collected from a subject using the kit may be received at a sample processing unit operatively coupled to a dispensing unit as described elsewhere herein. The sample processing unit may be operatively coupled to the dispensing unit wirelessly or through one or more wired interfaces. The sample processing unit may be operatively coupled to the dispensing unit through a network, such as the Internet or intranet.

The kit may be a commercially available kit. Alternatively, the kit may be a customary kit. The customary kit may be tailored for carrying out the at least one target assay.

Reagents and other materials in a kit may be contained in any suitable container, and may be in an immediately usable form or require combination with other reagents in the kit or reagents supplied by a user (e.g. dilution of a concentrated composition or reconstitution of a lyophilized composition) . A kit may provide buffers, non-limiting examples of which include sodium carbonate buffer, a sodium bicarbonate buffer, a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and combinations thereof. A kit may comprise a control sample, e.g., an analyte with known identity and quantity for control of sample preparation and/or assay execution for use as a positive control or quantification standard, or a blank sample known not to result in signals generated by the target assay for use as a negative control or blank control. In some embodiments, the kit comprises instructions for use of the kit in accordance with one or more assays disclosed herein. In some embodiments, a method for using the kit comprises any assay as described elsewhere herein.

Reagents

In another aspect, the present disclosure provides one or more reagents for collecting, processing and/or analyzing a biological sample of a subject. The one or more reagents may be necessary for processing a biological sample of the subject, in some cases based on selection by a user.

In some embodiments, the one or more reagents may be included in a kit as described elsewhere herein. For example, the one or more reagents may be included in one or more vials, such as at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 vials. The vials may be sealable, such as reversibly sealable. A vial may be sealed and accessible by breaking the seal.

In some embodiments, the one or more reagents may be selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for at least one target analyte.

In some embodiments, the one or more reagents may include a reverse transcriptase and a deoxyribonucleic acid (DNA) polymerase. The reverse transcriptase may be used to convert mRNA in a sample to cDNA for amplification or sequencing purpose.

In some embodiments, the one or more reagents may include reagents necessary for preserving the biological sample. As used herein, the term “preservation” or “preserving” indicates maintaining the bioactivity of the biological sample so as to allow assaying the biological sample after a time period, without significantly affecting the results of the assay as compared to assaying the biological sample immediately after collection. It is crucial for the biological sample to be preserved during storage and transportation before subject to detection and/or measurement as described herein to ensure the accuracy and relevance of the analysis of the biological sample. In some aspects, the biological samples are preserved for at least about 10 min, 30 min, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 12 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 6 months, 9 months, 1 year, or more than 1 year, or any time period between the time periods as enumerated above.

In some embodiments, the reagent may be a lysis buffer. The lysis buffer may comprise any suitable lysis agent, including commercially available lysis agents. Non-limiting examples of lysis agents include Tris-HCl, EDTA, detergents (e.g., Triton X-100, SDS) , lysozyme, glucolase, proteinase E, viral endolysins, exolysins, zymolase, lyticase, proteinase K, endolysins and exolysins from bacteriophages, endolysins from bacteriophage PM2, endolysins from the B. subtilis bacteriophage PBSX, endolysins from Lactobacillus prophages Lj928, Lj965, bacteriophage 15 Phiadh, endolysin from the Streptococcus pneumoniae bacteriophage Cp-I, bifunctional peptidoglycan lysin of Streptococcus agalactiae bacteriophage B30, endolysins and exolysins from prophage bacteria, endolysins from Listeria bacteriophages, holin-endolysin, cell 20 lysis genes, holWMY Staphylococcus wameri M phage varphiWMY, Iy5WMY of the Staphylococcus wameri M phage varphiWMY, Tween 20, PEG, KOH, NaCl, and combinations thereof. An example of a lysis buffer is sodium hydroxide (NaOH) . In some embodiments, the biological sample is not treated with a detergent. For example, the lysis buffer may not contain any detergent.

The lysis buffer may have a pH from about 7 to 14, such as from about 8 to 13, from about 9 to 12, from about 10 to 11. For example, the lysis buffer may have a pH of about 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5, 12, 12.5, 13, 13.5, or 14.

In any of the various aspects of the present disclosure, when the biological sample is mixed with a lysis buffer to obtain a mixture, a ratio of the biological sample to the lysis buffer may be between about 5: 1 (wt/vol) to about 1: 10 (wt/vol) , e.g., from about 1: 1 (wt/vol) to about 1: 10 (wt/vol) . For example, the ratio of the biological sample to the lysis buffer may be about 5: 1 (wt/vol) , about 4: 1 (wt/vol) , about 3: 1 (wt/vol) , about 2: 1 (wt/vol) , about 1: 1 (wt/vol) , about 1: 2 (wt/vol) , about 1: 3 (wt/vol) , about 1: 4 (wt/vol) , about 1: 5 (wt/vol) , about 1: 6 (wt/vol) , about 1: 7 (wt/vol) , about 1: 8 (wt/vol) , about 1: 9 (wt/vol) , or about 1: 10 (wt/vol) .

In some embodiments, the reagent may be a report agent. Reporter agents may be linked with nucleic acids, including amplified products, by covalent or non-covalent interactions. Non-limiting examples of non-covalent interactions include ionic interactions, Van der Waals forces, hydrophobic interactions, hydrogen bonding, and combinations thereof. In some embodiments, reporter agents may bind to initial reactants and changes in reporter agent levels may be used to detect amplified product. In some embodiments, reporter agents may only be detectable (or non-detectable) as nucleic acid amplification progresses. In some embodiments, an optically-active dye (e.g., a fluorescent dye) may be used as may be used as a reporter agent. Non-limiting examples of dyes include SYBR green, SYBR blue, DAPI, propidium iodine, Hoeste, SYBR gold, ethidium bromide, acridines, proflavine, acridine orange, acriflavine, fluorcoumanin, ellipticine, daunomycin, chloroquine, distamycin D, chromomycin, homidium, mithramycin, ruthenium polypyridyls, anthramycin, phenanthridines and acridines, ethidium bromide, propidium iodide, hexidium iodide, dihydroethidium, ethidium homodimer-1 and -2, ethidium monoazide, and ACMA, Hoechst 33258, Hoechst 33342, Hoechst 34580, DAPI, acridine orange, 7-AAD, actinomycin D, LDS751, hydroxystilbamidine, SYTOX Blue, SYTOX Green, SYTOX Orange, POPO-1, POPO-3, YOYO-1, YOYO-3, TOTO-1, TOTO-3, JOJO-1, LOLO-1, BOBO-1, BOBO-3, PO-PRO-1, PO-PRO-3, BO-PRO-1, BO-PRO-3, TO-PRO-1, TO-PRO-3, TO-PRO-5, JO-PRO-1, LO-PRO-1, YO-PRO-1, YO-PRO-3, PicoGreen, OliGreen, RiboGreen, SYBR Gold, SYBR Green I, SYBR Green II, SYBR DX, SYTO-40, -41, -42, -43, -44, -45 (blue) , SYTO-13, -16, -24, -21, -23, -12, -11, -20, -22, -15, -14, -25 (green) , SYTO-81, -80, -82, -83, -84, -85 (orange) , SYTO-64, -17, -59, -61, -62, -60, -63 (red) , fluorescein, fluorescein isothiocyanate (FITC) , tetramethyl rhodamine isothiocyanate (TRITC) , rhodamine, tetramethyl rhodamine, R-phycoerythrin, Cy-2, Cy-3, Cy-3.5, Cy-5, Cy5.5, , Cy-7, Texas Red, Phar-Red, allophycocyanin (APC) , Sybr Green I, Sybr Green II, Sybr Gold, CellTracker Green, 7-AAD, ethidium homodimer I, ethidium homodimer II, ethidium homodimer III, ethidium bromide, umbelliferone, eosin, green fluorescent protein, erythrosin, coumarin, methyl coumarin, pyrene, malachite green, stilbene, lucifer yellow, cascade blue, dichlorotriazinylamine fluorescein, dansyl chloride, fluorescent lanthanide complexes such as those including europium and terbium, carboxy tetrachloro fluorescein, 5 and/or 6-carboxy fluorescein (FAM) , 5- (or 6-) iodoacetamidofluorescein, 5- { [2 (and 3) -5- (Acetylmercapto) -succinyl] amino} fluorescein (SAMSA-fluorescein) , lissamine rhodamine B sulfonyl chloride, 5 and/or 6 carboxy rhodamine (ROX) , 7-amino-methyl-coumarin, 7-Amino-4-methylcoumarin-3-acetic acid (AMCA) , BODIPY fluorophores, 8-methoxypyrene-1, 3, 6-trisulfonic acid trisodium salt, 3, 6-Disulfonate-4-amino-naphthalimide, phycobiliproteins, AlexaFluor 350, 405, 430, 488, 532, 546, 555, 568, 594, 610, 633, 635, 647, 660, 680, 700, 750, and 790 dyes, DyLight 350, 405, 488, 550, 594, 633, 650, 680, 755, and 800 dyes, or other fluorophores.

In some embodiments, a reporter agent may be a sequence-specific oligonucleotide probe that is optically active when hybridized with an amplified product. Due to sequence-specific binding of the probe to the amplified product, use of oligonucleotide probes can increase specificity and sensitivity of detection. A probe may be linked to any of the optically-active reporter agents (e.g., dyes) described herein and may also include a quencher capable of blocking the optical activity of an associated dye. Non-limiting examples of probes that may be useful used as reporter agents include TaqMan probes, TaqMan Tamara probes, TaqMan MGB probes, or Lion probes.

In some embodiments and where a reporter agent may be an RNA oligonucleotide probe that includes an optically-active dye (e.g., fluorescent dye) and a quencher positioned adjacently on the probe. The close proximity of the dye with the quencher can block the optical activity of the dye. The probe may bind to a target sequence to be amplified. Upon the breakdown of the probe with the exonuclease activity of a DNA polymerase during amplification, the quencher and dye are separated, and the free dye regains its optical activity that can subsequently be detected.

In some embodiments, a reporter agent may be a molecular beacon. A molecular beacon includes, for example, a quencher linked at one end of an oligonucleotide in a hairpin conformation. At the other end of the oligonucleotide is an optically active dye, such as, for example, a fluorescent dye. In the hairpin configuration, the optically-active dye and quencher are brought in close enough proximity such that the quencher is capable of blocking the optical activity of the dye. Upon hybridizing with amplified product, however, the oligonucleotide assumes a linear conformation and hybridizes with a target sequence on the amplified product. Linearization of the oligonucleotide results in separation of the optically-active dye and quencher, such that the optical activity is restored and can be detected. The sequence specificity of the molecular beacon for a target sequence on the amplified product can improve specificity and sensitivity of detection.

In some embodiments, a reporter agent may be a radioactive species. Non-limiting examples of radioactive species include ¹⁴C’ ¹²³I’ ¹²⁴I’ ¹²⁵I’ ¹³¹I, Tc99m, ³⁵S, or ³H.

In some embodiments, a reporter agent may be an enzyme that is capable of generating a detectable signal. Detectable signal may be produced by activity of the enzyme with its substrate or a particular substrate in the case the enzyme has multiple substrates. Non-limiting examples of enzymes that may be used as reporter agents include alkaline phosphatase, horseradish peroxidase, I²-galactosidase, alkaline phosphatase, β-galactosidase, acetylcholinesterase, and luciferase.

In some embodiments, the reagent may be a DNA polymerase. Any suitable DNA polymerase may be used, including commercially available DNA polymerases. A DNA polymerase generally refers to an enzyme that is capable of incorporating nucleotides to a strand of DNA in a template bound fashion. Non-limiting examples of DNA polymerases include Taq polymerase, Tth polymerase, Tli polymerase, Pfu polymerase, VENT polymerase, DEEPVENT polymerase, EX-Taq polymerase, LA-Taq polymerase, Expand polymerases, Sso polymerase, Poc polymerase, Pab polymerase, Mth polymerase, Pho polymerase, ES4 polymerase, Tru polymerase, Tac polymerase, Tne polymerase, Tma polymerase, Tih polymerase, Tfi polymerase, Platinum Taq polymerases, Hi-Fi polymerase, Tbr polymerase, Tfl polymerase, Pfutubo polymerase, Pyrobest polymerase, Pwo polymerase, KOD polymerase, Bst polymerase, Sac polymerase, Klenow fragment, and variants, modified products and derivatives thereof. For certain Hot Start Polymerase, a denaturation step at 94℃ -95℃ for 2 minutes to 10 minutes may be required, which may change the thermal profile based on different polymerases.

In some embodiments, the reagent may be a reverse transcriptase. Any suitable reverse transcriptase may be used. A reverse transcriptase generally refers to an enzyme that is capable of incorporating nucleotides to a strand of DNA, when bound to an RNA template. Non-limiting examples of reverse transcriptases include HIV-1 reverse transcriptase, M-MLV reverse transcriptase, AMV reverse transcriptase, telomerase reverse transcriptase, and variants, modified products and derivatives thereof.

The reagent may be any reagent necessary for carrying out the at least one target assay as described elsewhere herein. The reagent may be one or more reagents necessary for carrying out a nucleic acid amplification assay, a sequencing assay, an immunoassay, an electrophoretic assay, an affinity assay, or any other assays suitable for the purpose of the present disclosure.

Target Analytes

Methods and systems of the present disclosure may be directed to determining a presence or absence, or amount, of at least one target analyte. The target analyte may be, for example, a biomarker, such as a biomarker as part of an organism (e.g., bacteria or virus) .

In some embodiments, the at least one target analyte is associated with a disease. The disease may be associated with a virus. The virus may be an RNA virus. The virus may be a DNA virus.

In some embodiments, the virus may be selected from the group consisting of human immunodeficiency virus I (HIV I) , human immunodeficiency virus II (HIV II) , an orthomyxovirus, Ebola virus, Dengue virus, influenza viruses, hepevirus, hepatitis A virus, hepatitis B virus, hepatitis C virus, hepatitis D virus, hepatitis E virus, hepatitis G virus, Epstein-Barr virus, mononucleosis virus, cytomegalovirus, SARS virus, West Nile Fever virus, polio virus, measles virus, herpes simplex virus, smallpox virus, adenovirus, Coxsackie virus, and Varicella virus.

In some embodiments, the influenza virus may be selected from the group consisting of H1N1 virus, H3N2 virus, H7N9 virus and H5N1 virus. The adenovirus may be adenovirus type 55 (ADV55) or adenovirus type 7 (ADV7) . The hepatitis C virus may be armored RNA-hepatitis C virus (RNA-HCV) . The Coxsackie virus may be Coxsackie virus A16.

In some embodiments, the disease may be associated with a pathogenic bacterium or a pathogenic protozoan. The pathogenic bacterium may be a gram-positive or gram-negative pathogenic bacterium. The pathogenic bacterium may be selected from the group consisting of Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Enterobacter sakazakii, Vibrio Parahemolyticus, and Shigella spp. The pathogenic bacterium may be Mycobacterium tuberculosis. The pathogenic protozoan may be Plasmodium. The pathogenic bacterium may be Salmonella.

In some embodiments, the disease may be an infection or an infectious disease. Infection typically refers to invasion and multiplication of infectious agents in body tissues of a subject, as well as reaction of host tissues to said infectious agents and toxins, if exists, produced by said infectious agents. An infectious disease is a disease caused by infection. Infectious diseases include, but are not limited to bacterial diseases, viral diseases, fungal infection, parasitic diseases, and the like.

In some embodiments, the infectious disease may be a bacterial disease. The bacterial disease may be a bacterial disease caused by Firmicutes. Firmicutes are a group of mostly Gram positive bacteria, but some of them may be Gram negative, characterized by low G+C contents. Firmicutes infectious diseases may include bacterial diseases caused by bacteria from the genera Streptococcus, Enterococcus, Staphylococcus, Bacillus, Listeria, Clostridium, Peptostreptoccous, Ureaplasma, Mycoplasma, Erysipelothrix, or the like.

Non-limiting examples of Firmicutes infectious diseases caused by Streptococcus include pneumococcal infection, infection caused by an optochin resistant (S. viridans, S. mitis, S. mutans, S. oralis, S. sanguinis, S. sobrinus, milleri group, etc. ) , Group A streptococcal infection, streptococcal pharyngitis, scarlet fever, erysipelas, rheumatic fever, Group B streptococcal infection, cutaneous Streptococcus iniae infection, Streoptoccus bovis infection, and the like. Non-limiting examples of Firmicutes infectious diseases caused by Enterococcus include urinary tract infection, Enterococcus faecium infection, and the like. Non-limiting examples of Firmicutes infectious diseases caused by Staphylococcus include staphylococcal scalded skin syndrome, toxic shock syndrome, Methicillin-resistant Staphylococcus aureus (MRSA) infection, infection caused by novobiocin susceptible and novobiocin resistant Cg-(coagulase negative) Staphyloccoccus, and the like. Non-limiting examples of Firmicutes infectious diseases caused by Bacillus include anthrax, food poisoning caused by Bacillus, and the like. Non-limiting examples of Firmicutes infectious diseases caused by Listeria include listeriosis and the like. Non-limiting examples of Firmicutes infectious diseases caused by Clostridium include pseudomembranous colitis, botulism, tetanus, gas gangrene, clostridial necrotizing enteritis, and the like. Non-limiting examples of Firmicutes infectious diseases caused by Peptostreptococcus include infection caused by Peptostreptococcus magnus and the like. Non-limiting examples of Firmicutes infectious diseases caused by Ureaplasma include ureaplasma infection and the like. Non-limiting examples of Firmicutes infectious diseases caused by Mycoplasma include mycoplasma pneumonia, infection caused by Mycoplasma genitalium, and the like. Non-limiting examples of Firmicutes infectious diseases caused by Erysipelothrix include erysipeloid and the like.

The bacterial disease may be a bacterial disease caused by Proteobacteria. Proteobacteria are a major group of Gram-negative bacteria. Proteobacteria can be further divided into Alphaprocteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria. Bacterial diseases caused by Proteobacteria can be caused by any of the aforesaid divisions.

Bacterial disease caused by Alphaproteobacteria may include those caused by genera Rickettsia, Orientia, Anaplasma, Ehrlichia, Brucella, Bartonella, or the like.

Non-limiting examples of bacterial diseases caused by Rickettsia include murine typhus, epidemic typhus, Brill-Zinsser disease, flying squirrel typhus, Rocky Mountain spotted fever, boutonneuse fever, Japanese spotted fever, North Asian tick typhus, Queensland tick typhus, Flinders Island spotted fever, African tick bite fever, American tick bite fever, Rickettsia aeschlimannii infection, rickettsialpox, flee-borne spotted fever, and the like. Non-limiting examples of bacterial diseases caused by Orientia include scrub typhus and the like. Non-limiting examples of bacterial diseases caused by Anaplasma include human granulocytic anaplasmosis, anaplasmosis, and the like. Non-limiting examples of bacterial diseases caused by Ehrlichia include human monocytotropic ehrlichiosis, Ehrlichiosis ewingii infection, and the like. Non-limiting examples of bacterial diseases caused by Brucella include brucellosis and the like. Non-limiting examples of bacterial diseases caused by Bartonellosis include cat-scratch disease, trench fever, bacillary angiomatosis, Carrion’s disease, verruga peruana, and the like.

Bacterial disease caused by Betaproteobacteria may include those caused by genera Neisseria, Eikenella, Chromobacerium, Burkholderia, or the like.

Non-limiting examples of bacterial diseases caused by Neisseria include meningococcal disease, Waterhouse-Friderichsen syndrome, meningococcal septicaemia, gonorrhea, and the like. Non-limiting examples of bacterial diseases caused by Eikenella include HACEK endocarditis and the like. Non-limiting examples of bacterial diseases caused by Chromobacterium include Chromobacteriosis infection and the like. Non-limiting examples of bacterial diseases caused by Burkholderia include melioidosis, glanders, infection caused by Burkholderia cepacia complex, pertussis, and the like.

Bacterial disease caused by Gammaproteobacteria may include those caused by genera Klebsiella, Escherichia, Enterobacter, Serratia, Salmonella, Shigella, Proteus, Yersinia, Haemophilus, Pasteurella, Actinobacillus, Aggregatibacter, Legionella, Coxiella, Francisella, Vibrio, Plesiomonas, Pseudomonas, Moraxella, Acinetobacter, Stenotrophomonas, Cardiobacterium, Aeromonas, or the like.

Non-limiting examples of bacterial diseases caused by Klebsiella include rhinoscleroma, Klebsiella pneumonia, donovanosis or granuloma inguinale, infection caused by Klebsiella oxytoca, and the like. Non-limiting examples of bacterial diseases caused by Escherichia include infection caused by E. coli (enterotoxigenic, enteroinvasive, enterohemorrhagic, O157: H7, O104: H4) , hemolytic-uremic syndrome, and the like. Non-limiting examples of bacterial diseases caused by Serratia include Serratia infection and the like. Non-limiting examples of bacterial diseases caused by Citrobacter include infection caused by Citrobacter koseri/Citrobacter freundii. Non-limiting examples of bacterial diseases caused by Salmonella include typhoid fever, paratyphoid fever, salmonellosis, and the like. Non-limiting examples of bacterial diseases caused by Shigella include Shigellosis, bacillary dysentery, and the like. Non-limiting examples of bacterial diseases caused by Proteus include infection caused by Proteus mirabillis/Proteus vulgaris and the like. Non-limiting examples of bacterial diseases caused by Yersinia include plague/bubonic plague, yersiniosis, Far East scarlet-like fever, and the like. Non-limiting examples of bacterial diseases caused by Haemophilus include haemophilus meningitis, Brazian purpuric fever, chancroid, HACEK endocarditis, and the like. Non-limiting examples of bacterial diseases caused by Pasteurella include pasteurellosis and the like. Non-limiting examples of bacterial diseases caused by Actinobacillus include actinobacillosis and the like. Non-limiting examples of bacterial diseases caused by Aggregatibacter include HACEK endocarditis and the like. Non-limiting examples of bacterial diseases caused by Legionella include legionnaires’disease and the like. Non-limiting examples of bacterial diseases caused by Coxiella include Q fever and the like. Non-limiting examples of bacterial diseases caused by Francisella include tularemia and the like. Non-limiting examples of bacterial diseases caused by Vibrio include cholera, infection caused by other Vibrio species (V. vulnificus, V. parahaemolyticus, V. alginolyticus, and the like) , and the like. Non-limiting examples of bacterial diseases caused by Plesiomonas include infection caused by Plesiomonas shigelloides and the like. Non-limiting examples of bacterial diseases caused by Pseudomonas include pseudomonas infection and the like. Non-limiting examples of bacterial diseases caused by Moraxella include infection caused by Moraxella catarrhalis and the like. Non-limiting examples of bacterial diseases caused by Acinetobacter include infection caused by Acinetobacter baumannii and the like. Non-limiting examples of bacterial diseases caused by Stenotrophomonas include infection caused by Stenotrophomonas maltophilia and the like. Non-limiting examples of bacterial diseases caused by Cardiobacterium include HACEK endocarditis and the like. Non-limiting examples of bacterial diseases caused by Aeromonas include Aeromonas infection and the like.

Bacterial disease caused by Epsilonproteobacteria may include those caused by genera Campylobacter, Helicobacter, or the like.

Non-limiting examples of bacterial diseases caused by Campylobacter include campylobacteriosis, Guillan-Barre syndrome, and the like. Non-limiting examples of bacterial diseases caused by Helicobacter include peptic ulcer, MALT lymphoma, gastric cancer, helicobacter cellulitis, and the like.

The bacterial disease may be a bacterial disease caused by a non-Proteobacteria Gram-negative bacterium. Bacterial disease caused by non-proteobacteria Gram-negative bacteria may include those caused by genera Treponema, Borrelia, Leptospira, Spirillum, Chlamydophila, Chlamydia, Bacteroides, Tannerella, Capnocytophaga, Porphyromonas, Prevotella, Fusobacterium, Streptobacillus, or the like.

Non-limiting examples of bacterial diseases caused by Treponema include syphilis/bejel, yaws, pinta, infection caused by Treponema denticola, and the like. Non-limiting examples of bacterial diseases caused by Borrelia include lyme disease, erythema chronicum migrans, neuboborreliosis, louse borne relapsing fever, tick borne relapsing fever, and the like. Non-limiting examples of bacterial diseases caused by Leptospira include leptosipirosis and the like. Non-limiting examples of bacterial diseases caused by Spirillum include rat-bite fever/sodoku and the like. Non-limiting examples of bacterial diseases caused by Chlamydophila includepsittacosis, infection caused by pneumoniae, and the like. Non-limiting examples of bacterial diseases caused by Chlamydia include chlamydia, lymphogranuloma venereum, trachoma, and the like. Non-limiting examples of bacterial diseases caused by Bacteroides include infection caused by Bacteroides fragilis and the like. Non-limiting examples of bacterial diseases caused by Tannerella include infection caused by Tannerella forsythia and the like. Non-limiting examples of bacterial diseases caused by Capnocytophaga include infection caused by Capnocytophaga canimorsus and the like. Non-limiting examples of bacterial diseases caused by Porphyromonas include infection caused by Porphyromonas gingivalis and the like. Non-limiting examples of bacterial diseases caused by Prevotella include infection caused by Prevotella intermedia and the like. Non-limiting examples of bacterial diseases caused by Fusobacterium include lemierre’s syndrome, infection caused by Fusobacterium nucleatum and Fusobacterium polymorphum, and the like. Non-limiting examples of bacterial diseases caused by Streptobacillus include rat-bite fever/haverhill fever and the like.

In some embodiments, the infectious disease is a viral disease.

The viral disease may be a neoplasm caused by an oncovirus. Non-limiting examples of neoplasms caused by oncoviruses include heptaocellular carcinoma, cervical cancer, anal cancer, penile cancer, vulvar cancer, vaginal cancer, oropharyngeal cancer, Kaposi’s sarcoma, nasopharynx cancer, Burkitt’s lymphoma, Hodgkin’s limphma, follicular dendritic cell sarcoma, nasal type NK/T-cell lymphoma, Merkel cell carcinoma, heptocellular carcinoma, splenic marginal zone lymphoma, adult T-cell leukemia/lymphoma, and the like.

The viral disease may be an immune disorder such as acquired immune deficiency syndrom (AIDS) , and the like.

The viral disease may be a central nervous system or eye viral disease. Non-limiting examples of central nervous system or eye viral diseases include progressive multifocal leukoencephalopathy, subacute slerosing panencephalitis, lymphocitic choriomeningitis, arbovirus encephalitis, encephalitis lethargica, rabies, infection caused by Chandipura virus, herpesviral meningitis, Ramsay Hunt syndrome type II, poliomyelitis, post-polio syndrome, tropical spastic paraparesis, cytomegalovirus retinitis, herpes of the eye, and the like.

The viral disease may be a cardiovascular viral disease. Non-limiting examples of cardiovascular viral diseases include pericarditis, myocarditis, and the like.

The viral disease may be a respiratory system viral disease such as an acute viral nasopharyngitis or viral pneumonia. Non-limiting examples of respiratory system viral diseases include EBV infection/infectious mononucleosis, infection caused by Cytomegalovirus, severe acute respiratory syndrome (SARS) , influenza, avian influenza, parainfluenza, infection caused by human respiratory syncytial virus (RSF) , infection caused by human metapneumovirus (hMPV) , and the like.

The viral disease may be a digestive system viral disease. Non-limiting examples of digestive system viral diseases include mumps, cytomegalovirus esophagitis, gastroenteritis/diarrhea caused by a DNA virus (adenovirus infection or the like) , gastroenteritis/diarrhea caused by an RNA virus (Rotavirus, Norovirus, Astrovirus, Coronavirus, or the like) , hepatitis caused by a DNA virus (hepatitis B) , hepatitis caused by an RNA virus (hepatitis A, hepatitis C, hepatitis D, hepatitis E, hepatitis G, or the like) , hepatitis or pancreatitis caused by Coxsackie B virus (CBV) , and the like.

The viral disease may be a urogenital viral disease. Non-limiting examples of urogenital viral diseases include infection caused by BK virus, mumps, and the like.

In some embodiments, the infectious disease is a parasitic disease caused by protozoa such as trichomoniasis.

In some embodiments, the infectious disease is a fungal infection. Fungi include Ascomycota, Basidiomycota, Zygomycota, and Microsporidia. In the context of this disclosure, the term “fungus/fungi” also encompasses mesomycetozoa. Therefore, infection caused by mesomycetozoea such as phinosporidiosis is also encompassed in the scope of this disclosure.

Non-limiting examples of fungal infections caused by Ascomycota include tinea barbae/tineacapitis (kerion) , tinea corporis (ringworm or dermatophytids) , tinea cruris, tinea manuum, tinea pedis (athlete’s foot) , tinea unguium/onychomycosis (white superficial onychomycosis, distal subungual onychomycosis, proximal subungual onychomycosis) , tinea corporis gladiatorum, tinea faciel, tinea imbricata, tinea incognito, favus, tinea nigra, black piedra, coccidioidomycosis, disseminated coccidioidomycosis, primary cutaneous coccidioidomycosis, primary pulmonary coccidioidomycosis, histoplasmosis, primary cutaneous histoplasmosis, primary pulmonary histoplasmosis, progressive dissemniated histoplasmosis, African histoplasmosis, lobomycosis, paracoccidioidomycosis, blastomycosis, North American blastomycosis, South American blastomycosis, sporotrichosis, penicilliosis, candidiasis, oral candidiasis, esophageal candidiasis, vulvovaginal candidiasis, chronic mucocutaneous candidiasis, antibiotic candidiasis, candidal intertrigo, candidal onychomycosis, candidal paronychia, candidid, diaper candidiasis, congenital cutaneous candidiasis, perianal candidiasis, systemic candidiasis, erosio interdigitalis blastomycetica, pneumocystosis, pneumocystis pneumonia, aspergillosis, aspergilloma, allergic bronchopulmonary aspergillosis, primary cutaneous aspergillosis, eumycetoma, chromoblastomycosis geotrichosis, allescheriasis, and the like.

Non-limiting examples of fungal infections caused by Basidiomycota include tinea versicolor, pityrosporium folliculitis, white piedra, cryptococcosis, trichosporonosis, and the like.

Non-limiting examples of fungal infections caused by Zygomycota include mucormycosis, entomophthoramycosis such as basidobolomycosis and conidiobolomycosis, and the like.

Non-limiting examples of fungal infections caused by Microsporidia include microsporidiosis caused by Enterocytozoon bieneusi/Encephalitozoon intestinalis, and the like.

In addition, further non-limiting examples of infectious diseases include Acinetobacter infections, Actinomycosis, African sleeping sickness (African trypanosomiasis) , AIDS (Acquired immunodeficiency syndrome) , Amebiasis, Anaplasmosis, Angiostrongyliasis, Anisakiasis, Anthrax, Arcanobacterium haemolyticum infection, Argentine hemorrhagic fever, Ascariasis, Aspergillosis, Astrovirus infection, Babesiosis, Balantidiasis, Bartonellosis Baylisascaris infection, BK virus infection, Black piedra, Blastocystis hominis infection, Blastomycosis, Bolivian hemorrhagic fever, Botulism (and Infant botulism) , Brazilian hemorrhagic fever, Brucellosis, Bubonic plague, Burkholderia infection, Buruli ulcer, Calicivirus infection (Norovirus and Sapovirus) , Campylobacteriosis, Candidiasis (Moniliasis； Thrush) , Capillariasis, Carrion′s disease, Cat-scratch disease, Cellulitis, Chagas Disease (American trypanosomiasis) , Chancroid, Chickenpox, Chikungunya, Chlamydia, Chlamydophila pneumoniae infection (Taiwan acute respiratory agent or TWAR) , Cholera, Chromoblastomycosis, Clonorchiasis, Clostridium difficile infection, Coccidioidomycosis, Colorado tick fever (CTF) , Common cold (Acute viral rhinopharyngitis； Acute coryza) , Creutzfeldt-Jakob disease (CJD) , Crimean-Congo hemorrhagic fever (CCHF) , Cryptococcosis, Cryptosporidiosis, Cutaneous larva migrans (CLM) , Cyclosporiasis, Cysticercosis, Cytomegalovirus infection, Dengue fever, Desmodesmus infection, Dientamoebiasis, Diphtheria, Diphyllobothriasis, Dracunculiasis, Ebola hemorrhagic fever, Echinococcosis, Ehrlichiosis, Enterobiasis (Pinworm infection) , Enterococcus infection, Enterovirus infection, Epidemic typhus, Erythema infectiosum (Fifth disease) , Exanthem subitum (Sixth disease) , Fasciolasis, Fasciolopsiasis, Fatal familial insomnia (FFI) , Filariasis, Food poisoning by Clostridium perfringens, Free-living amebic infection, Fusobacterium infection, Gas gangrene (Clostridial myonecrosis) , Geotrichosis, Gerstmann-

-Scheinker syndrome (GSS) , Giardiasis, Glanders, Gnathostomiasis, Gonorrhea, Granuloma inguinale (Donovanosis) , Group A streptococcal infection, Group B streptococcal infection, Haemophilus influenzae infection, Hand, foot and mouth disease (HFMD) , Hantavirus Pulmonary Syndrome (HPS) , Heartland virus disease, Helicobacter pylori infection, Hemolytic-uremic syndrome (HUS) , Hemorrhagic fever with renal syndrome (HFRS) , Hepatitis A, Hepatitis B, Hepatitis C, Hepatitis D, Hepatitis E, Herpes simplex, Histoplasmosis, Hookworm infection, Human bocavirus infection, Human ewingii ehrlichiosis, Human granulocytic anaplasmosis (HGA) , Human metapneumovirus infection, Human monocytic ehrlichiosis, Human papillomavirus (HPV) infection, Human parainfluenza virus infection, Hymenolepiasis, Epstein-Barr Virus Infectious, Mononucleosis (Mono) , Influenza (flu) , Isosporiasis, Kawasaki disease, Keratitis, Kingella kingae infection, Kuru Lassa fever Legionellosis (Legionnaires'disease) , Legionellosis (Pontiac fever) , Leishmaniasis, Leprosy, Leptospirosis, Listeriosis, Lyme disease (Lyme borreliosis) , Lymphatic filariasis (Elephantiasis) , Lymphocytic choriomeningitis, Malaria, Marburg hemorrhagic fever (MHF) , Measles, Middle East respiratory syndrome (MERS) , Melioidosis (Whitmore's disease) , Meningitis, Meningococcal disease, Metagonimiasis, Microsporidiosis, Molluscum contagiosum (MC) , Monkeypox, Mumps, Murine typhus (Endemic typhus) , Mycoplasma pneumonia, Mycetoma (disambiguation) , Myiasis, Neonatal conjunctivitis (Ophthalmia neonatorum) , (New) Variant Creutzfeldt-Jakob disease (vCJD, nvCJD) , Nocardiosis Onchocerciasis (River blindness) , Opisthorchiasis, Paracoccidioidomycosis (South American blastomycosis) , Paragonimiasis, Pasteurellosis, Pediculosis capitis (Head lice) , Pediculosis corporis (Body lice) , Pediculosis pubis (Pubic lice, Crab lice) , Pelvic inflammatory disease (PID) , Pertussis (Whooping cough) , Plague Pneumococcal infection, Pneumocystis pneumonia (PCP) , Pneumonia Poliomyelitis Prevotella infection, Primary amoebic meningoencephalitis (PAM) , Progressive multifocal leukoencephalopathy, Psittacosis Q fever, Rabies, Relapsing fever, Respiratory syncytial virus infection, Rhinosporidiosis, Rhinovirus infection, Rickettsial infection, Rickettsialpox Rift Valley fever (RVF) , Rocky Mountain spotted fever (RMSF) , Rotavirus infection, Rubella Salmonellosis, SARS (Severe Acute Respiratory Syndrome) , Scabies Schistosomiasis, Sepsis, Shigellosis, (Bacillary dysentery) , Shingles (Herpes zoster) , Smallpox (Variola) , Sporotrichosis, Staphylococcal food poisoning, Staphylococcal infection, Strongyloidiasis, Subacute sclerosing panencephalitis, Syphilis Taeniasis, Tetanus (Lockjaw) , Tinea barbae (Barber's itch) , Tinea capitis (Ringworm of the Scalp) , Tinea corporis (Ringworm of the Body) , Tinea cruris (Jock itch) , Tinea manum (Ringworm of the Hand) , Tinea nigra, Tinea pedis (Athlete’s foot) , Tinea unguium (Onychomycosis) , Tinea versicolor (Pityriasis versicolor) , Toxocariasis (Ocular Larva Migrans (OLM) ) , Toxocariasis (Visceral Larva Migrans (VLM) ) , Trachoma, Toxoplasmosis, Trichinosis, Trichomoniasis, Trichuriasis (Whipworm infection) , Tuberculosis, Tularemia, Typhoid fever, Typhus fever, Ureaplasma urealyticum infection, Valley fever, Venezuelan equine encephalitis, Venezuelan hemorrhagic fever, Vibrio vulnificus infection, Vibrio parahaemolyticus enteritis, Viral pneumonia, West Nile Fever, White piedra (Tinea blanca) , Yersinia pseudotuberculosis infection, Yersiniosis, Yellow fever, and Zygomycosis.

In some embodiments, the disease, condition or disorder may be a disease, condition or disorder associated with dysbiosis, or microbial imbalance. When the balance among colonies is disturbed, these colonies exhibit a decreased ability to check each other’s growth, which can then lead to overgrowth of one or more of the disturbed colonies which may further damage some of the other smaller beneficial ones. As more beneficial colonies are damaged, making the imbalance more pronounced, more overgrowth issues occur because the damaged colonies are less able to check the growth of the overgrowing colonies. The disease, condition or disorder associated with microbial imbalance includes, but is not limited to obesity； malnutrition； diabetes (both type-1 and type-2) ； atherosclerosis and heart disease； multiple sclerosis； asthma and eczema； liver disease； numerous diseases of the intestines, including bowel cancer； and autism.

Alternatively, the target analyte may be associated with a beneficial microbe.

In some embodiments, the beneficial microbe may be a bacterium, fungus, protozoon, or virus. In some embodiments, the beneficial microbe is selected from the group consisting of: Escherichia coli, Paracolon, Enterobacter aerogenes, Proteus, Pseudomonas aeruginosa, pneumobacillus, Bacillus, Saccharomyces, Bacteroides, Bifidobacterium, Clostridium, Collinsella, Lactobacillus, Ruminococcus, Enterococcus, Hirsutellia, Lactobacillus, Dorea, Listeria, Streptococcus, Staphyloccocus, Corynebacterium, Propionibacterium, Clostridium butyricum, Streptococcus, Staphylococcus, Candida albicans, Fungus, Campylobacter, and Bacteriophages.

Biological Sample

In some aspect, the present disclosure involves one or more biological samples.

Any suitable biological sample that comprises nucleic acid may be obtained from a subject. A biological sample may be solid matter (e.g., biological tissue) or may be a fluid (e.g., a biological fluid) . In general, a biological fluid can include any fluid associated with living organisms. Non-limiting examples of a biological sample include blood (or components of blood –e.g., white blood cells, red blood cells, platelets) obtained from any anatomical location (e.g., tissue, circulatory system, bone marrow) of a subject, cells obtained from any anatomical location of a subject, skin, heart, lung, kidney, breath, bone marrow, stool, semen, vaginal fluid, interstitial fluids derived from tumorous tissue, breast, pancreas, cerebral spinal fluid, tissue, throat swab, biopsy, placental fluid, amniotic fluid, liver, muscle, smooth muscle, bladder, gall bladder, colon, intestine, brain, cavity fluids, sputum, pus, microbiota, meconium, breast milk, prostate, esophagus, thyroid, serum, saliva, urine, gastric and digestive fluid, tears, ocular fluids, sweat, mucus, earwax, oil, glandular secretions, spinal fluid, hair, fingernails, skin cells, plasma, nasal swab or nasopharyngeal wash, spinal fluid, cord blood, lymphatic fluids, and/or other excretions or body tissues. In an example, the biological sample is a stool sample.

In other cases, the biological sample may be from a soil or food sample. For example, the food sample may be a dairy sample and in some cases, the diary sample may include milk.

A biological sample may be obtained from a subject using various approaches. Non-limiting examples of approaches to obtain a biological sample directly from a subject include accessing the circulatory system (e.g., intravenously or intra-arterially via a syringe or other needle) , collecting a secreted biological sample (e.g., feces, urine, sputum, saliva, etc. ) , surgically (e.g., biopsy) , swabbing (e.g., buccal swab, oropharyngeal swab, rectal swab) , pipetting, and breathing. Moreover, a biological sample may be obtained from any anatomical part of a subject where a desired biological sample is located. In some embodiments, the biological sample may be obtained from a container thereof, e.g., a container (e.g., a bag, a box or a bottle) comprising food (e.g., milk) or soil. Soil may be mixture of minerals, organic matter, gases, liquids, and in some cases organisms.

In some cases, the biological sample is obtained directly from the subject. A biological sample obtained directly from a subject generally refers to a biological sample that has not been further processed after being obtained from the subject, with the exception of any approach used to collect the biological sample from the subject for further processing. For example, blood is obtained directly from a subject by accessing the subject’s circulatory system, removing the blood from the subject (e.g., via a needle) , and entering the removed blood into a receptacle. The receptacle may comprise reagents (e.g., anti-coagulants) such that the blood sample is useful for further analysis. In another example, a swab may be used to access epithelial cells on an oropharyngeal surface of the subject. In a further example, a swab may be used to access stool samples of the subject. After obtaining the biological sample from the subject, the swab containing the biological sample can be contacted with a fluid (e.g., a buffer) to collect the biological fluid from the swab. In another example, food (e.g., milk) may be obtained directly from a source thereof (e.g., a container comprising the food) by accessing the food in the source, removing the food from the container (e.g., by pipetting) , and entering the removed food into a receptacle.

Nucleic Acid Amplification and Detection

The present disclosure provides methods for nucleic acid amplification and detection. Such methods may be used to detect a presence or absence, or amount, of one or more analytes. The one or more analytes may include a target analyte.

In another aspect, the present disclosure provides a method for detecting a target nucleic acid molecule in a biological sample. The method may comprise: (a) mixing said biological sample with a lysis buffer to obtain a mixture； (b) incubating said mixture at a temperature from about 15℃ to 70℃ for a period of time of no more than about 15 minutes； (c) adding said mixture from (b) to a reaction vessel comprising reagents necessary for conducting nucleic acid amplification, said reagents comprising (i) a deoxyribonucleic acid (DNA) polymerase, and (ii) a primer set for said target nucleic acid molecule, to obtain a reaction mixture； and (d) subjecting said reaction mixture in said reaction vessel to multiple cycles of a primer extension reaction to generate amplified product (s) that is indicative of a presence of said target nucleic acid molecule, each cycle comprising (i) incubating said reaction mixture at a denaturing temperature for a denaturing duration that is less than or equal to 60 seconds, followed by (ii) incubating said reaction mixture at an elongation temperature for an elongation duration that is less than or equal to 60 seconds, thereby amplifying said target nucleic acid molecule. The amplified product may be DNA product.

In another aspect, the present disclosure provides a method for detecting a target nucleic acid molecule in a biological sample. The method may comprise: (a) mixing said biological sample with a lysis buffer to obtain a mixture； (b) incubating said mixture at a temperature from about 15℃ to 70℃ for a period of time of no more than about 15 minutes； (c) adding said mixture from (b) to a reaction vessel comprising reagents necessary for conducting nucleic acid amplification, said reagents comprising (i) a deoxyribonucleic acid (DNA) polymerase and optionally a reverse transcriptase, and (ii) a primer set for said target nucleic acid molecule, to obtain a reaction mixture； and (d) subjecting said reaction mixture in said reaction vessel to a plurality of series of primer extension reactions to generate amplified product (s) that is indicative of a presence of said target nucleic acid molecule in said sample, each series comprising two or more cycles of (i) incubating said reaction mixture under a denaturing condition characterized by a denaturing temperature and a denaturing duration, followed by (ii) incubating said reaction mixture under an elongation condition characterized by an elongation temperature and an elongation duration, wherein an individual series differs from at least one other individual series of said plurality with respect to said denaturing condition and/or said elongation condition. The amplified product may be DNA product.

In another aspect, the present disclosure provides a method for detecting a target nucleic acid molecule in a biological sample. The method may comprise (a) mixing said biological sample with a lysis buffer to obtain a mixture, wherein said biological sample includes a stool sample or milk sample； (b) incubating said mixture at an incubation temperature for an incubation time period； (c) adding said mixture from (b) to a reaction vessel comprising reagents necessary for conducting nucleic acid amplification, said reagents comprising (i) a deoxyribonucleic acid (DNA) polymerase, and (ii) a primer set for said target nucleic acid molecule, to obtain a reaction mixture； and (d) subjecting said reaction mixture in said reaction vessel to multiple cycles of a primer extension reaction to generate amplified product (s) that is indicative of a presence of said target nucleic acid molecule, each cycle comprising (i) incubating said reaction mixture at a denaturing temperature for a denaturing duration that is less than or equal to 60 seconds, followed by (ii) incubating said reaction mixture at an elongation temperature for an elongation duration that is less than or equal to 60 seconds, thereby amplifying said target nucleic acid molecule. The amplified product may be DNA product.

In another aspect, the present disclosure provides a method for detecting a target nucleic acid molecule in a biological sample. The method may comprise: (a) mixing said biological sample with a lysis buffer to obtain a mixture, wherein said biological sample includes a stool sample or milk sample； (b) incubating said mixture at an incubation temperature for an incubation time period； (c) adding said mixture from (b) to a reaction vessel comprising reagents necessary for conducting nucleic acid amplification, said reagents comprising (i) a deoxyribonucleic acid (DNA) polymerase and optionally a reverse transcriptase, and (ii) a primer set for said target nucleic acid molecule, to obtain a reaction mixture； and (d) subjecting said reaction mixture in said reaction vessel to a plurality of series of primer extension reactions to generate amplified product (s) that is indicative of a presence of said target nucleic acid molecule in said sample, each series comprising two or more cycles of (i) incubating said reaction mixture under a denaturing condition characterized by a denaturing temperature and a denaturing duration, followed by (ii) incubating said reaction mixture under an elongation condition characterized by an elongation temperature and an elongation duration, wherein an individual series differs from at least one other individual series of said plurality with respect to said denaturing condition and/or said elongation condition. The amplified product may be DNA product.

In any of the various aspects of the present disclosure, the “incubation temperature” may be from about 10℃ to 75℃, for example, at a temperature that is from about 10℃ to 70℃, from about 15℃ to 65℃, from about 15℃ to 60℃, from about 15℃ to 55℃, from about 20℃ to 50℃, from about 20℃ to 45℃, from about 20℃ to 40℃, from about 20℃ to 35℃, from about 20℃ to 30℃, from about 20℃ to 25℃, or from about 25℃ to 30℃.

In any of the various aspects of the present disclosure, the “incubation time period” may be no more than about 20 minutes. For example, the “incubation time period” may be no more than about 19 minutes, no more than about 18 minutes, no more than about 17 minutes, no more than about 16 minutes, no more than about 15 minutes, no more than about 14 minutes, no more than about 13 minutes, no more than about 12 minutes, no more than about 11 minutes, no more than about 10 minutes, no more than about 9 minutes, no more than about 8 minutes, no more than about 7 minutes, no more than about 6 minutes, no more than about 5 minutes, no more than about 4 minutes, no more than about 3 minutes, no more than about 2 minutes, no more than about 1 minute, no more than about 50 seconds, no more than about 40 seconds, no more than about 30 seconds, no more than about 20 seconds, no more than about 15 seconds, or no more than about 10 seconds.

In any of the various aspects of the present disclosure, prior to mixing the biological sample with a lysis buffer, the biological sample may be suspended in solution to obtain a homogenized preparation comprising the biological sample. In some embodiments, prior to being mixed with a lysis buffer, the biological sample is subjected to centrifugation to yield a solution comprising the biological sample and a pellet. In some embodiments, prior to being mixed with a lysis buffer, the biological sample is subjected to centrifugation to yield a pellet comprising the biological sample and a supernatant.

In some embodiments, after incubating the mixture of the biological sample and the lysis buffer, the mixture may be subjected to centrifugation to yield a supernatant comprising the biological sample. Then, the supernatant may be added to a reaction vessel comprising reagents necessary for conducting nucleic acid amplification.

In some cases, before conducting the primer extension reactions, the target nucleic acid molecules may be subjected to one or more denaturing conditions. The one or more denaturing conditions may be selected from a denaturing temperature profile and a denaturing agent.

In some cases, before conducting the primer extension reactions, the biological sample may be pre-heated at a pre-heating temperature from 90℃ to 100℃ for a pre-heating duration of no more than 10 minutes. In some embodiments, the pre-heating duration is no more than 1 minute.

In any of the various aspects of the present disclosure, the mixture of the biological sample with the lysis buffer may be added to the reaction vessel comprising reagents necessary for conducting nucleic acid amplification without undergoing DNA or ribonucleic acid (RNA) extraction. In some cases, the mixture may be added to the reaction vessel without undergoing purification. In certain cases, the mixture may be added to the reaction vessel without undergoing DNA or RNA concentration.

In any of the various aspects of the present disclosure, the mixture of the biological sample with the lysis buffer may be incubated at a temperature that is from about 10℃ to 75℃, for example, at a temperature that is from about 10℃ to 70℃, from about 15℃ to 65℃, from about 15℃ to 60℃, from about 15℃ to 55℃, from about 20℃ to 50℃, from about 20℃ to 45℃, from about 20℃ to 40℃, from about 20℃ to 35℃, from about 20℃ to 30℃, from about 20℃ to 25℃, or from about 25℃ to 30℃.

In any of the various aspects of the present disclosure, the mixture of the biological sample with the lysis buffer may be incubated for a period of time that is no more than about 20 minutes. For example, the period of time in (b) may be no more than about 19 minutes, no more than about 18 minutes, no more than about 17 minutes, no more than about 16 minutes, no more than about 15 minutes, no more than about 14 minutes, no more than about 13 minutes, no more than about 12 minutes, no more than about 11 minutes, no more than about 10 minutes, no more than about 9 minutes, no more than about 8 minutes, no more than about 7 minutes, no more than about 6 minutes, no more than about 5 minutes, no more than about 4 minutes, no more than about 3 minutes, no more than about 2 minutes, no more than about 1 minute, no more than about 50 seconds, no more than about 40 seconds, no more than about 30 seconds, no more than about 20 seconds, no more than about 15 seconds, or no more than about 10 seconds.

In any of the various aspects of the present disclosure, nucleic acid from a biological sample obtained from a subject is amplified. The biological sample may be obtained directly from a source thereof. For example, the biological sample may be obtained directly from a source thereof without pre-culturing, non-selective enrichment, selective enrichment, plating on differential medium, and/or presumptive biomedical identification. “Pre-culturing” generally refers to a process for expanding one or more target species (e.g., microorganisms) in a sample, or for increasing the number thereof, prior to performing methods of the present disclosure. “Non-selective enrichment” generally refers to a process of increasing the amount of a majority or all of the species (e.g., microorganisms) in a mixed population non-selectively. “Selective enrichment” generally refers to a process of increasing the proportion and/or amount of one or more specific species (e.g., microorganisms) in a mixed population while inhibiting other species. Such inhibition may result due to medium constituents such as compounds which are selectively toxic, as well as the end-products of microbial metabolism produced by organisms which utilize the medium constituents. “Differential medium” generally refers to a medium that includes one or more added indicator (s) that allows for the differentiation of particular chemical reactions occurring during growth. “Presumptive biomedical identification” generally refers to preliminary identification of a microorganism based on observation such as colony characteristics, growth on primary isolation media, gram stain results, etc.

In some embodiments, prior to being mixed with a lysis buffer, the biological sample is subjected to enrichment culturing conditions for a culturing time period. The enrichment culturing conditions may comprise culturing the biological sample in a suitable culture medium (e.g., tryptic soy broth, modified tryptic soy broth, tryptone, nutrient broth, L-broth, gram negative broth, peptone, or tryptic soy broth with yeast) at a suitable temperature (e.g., from 23℃to 40℃, such as 25℃, 30℃, 35℃, or 37℃) with or without shaking. The culturing time period may be from about 0.5 hour to 5 hours, e.g., about 1 hour, about 1.5 hours, about 2 hours, about 2.5 hours, about 3 hours, about 3.5 hours, about 4 hours, about 4.5 hours, or about 5 hours. In some embodiments, the culturing time period is no more than about 3 hours, e.g., no more than about 2.5 hours, no more than about 2 hours, no more than about 1.5 hours, no more than about 1 hour, no more than about 0.5 hour.

In some embodiments, prior to and/or after being subjected to enrichment culturing conditions for a culturing time period, the biological sample is subjected to centrifugation to yield a solution comprising the biological sample and a pellet. In some embodiments, prior to and/or after being subjected to enrichment culturing conditions for a culturing time period, the biological sample is subjected to centrifugation to yield a pellet comprising the biological sample and a supernatant.

In some embodiments, after being subjected to enrichment culturing conditions for a culturing time period, the biological sample is mixed with the lysis buffer without selective enrichment, plating on differential medium, and/or presumptive biomedical identification.

In some embodiments, a biological sample has not been purified when provided in a reaction vessel. In some embodiments, the nucleic acid of a biological sample has not been extracted when the biological sample is provided to a reaction vessel. For example, the RNA or DNA in a biological sample may not be extracted from the biological sample when providing the biological sample to a reaction vessel. Moreover, in some embodiments, a target nucleic acid (e.g., a target RNA or target DNA) present in a biological sample may not be concentrated prior to providing the biological sample to a reaction vessel.

In any of the various aspects, a target nucleic acid is amplified to generate an amplified product. A target nucleic acid may be a target RNA or a target DNA. The target nucleic acid molecule may be associated with a disease. In cases where the target nucleic acid is a target RNA, the target RNA may be any type of RNA, including types of RNA described elsewhere herein. In some embodiments, the target RNA is viral RNA. In some embodiments, the viral RNA may be pathogenic to the subject. Non-limiting examples of pathogenic viral RNA include human immunodeficiency virus I (HIV I) , human immunodeficiency virus II (HIV II) , orthomyxoviruses, Ebola virus, Dengue virus, influenza viruses (e.g., H1N1, H3N2, H7N9, or H5N1) , hepesvirus, hepatitis A virus, hepatitis B virus, hepatitis C (e.g., armored RNA-HCV virus) virus, hepatitis D virus, hepatitis E virus, hepatitis G virus, Epstein-Barr virus, mononucleosis virus, cytomegalovirus, SARS virus, West Nile Fever virus, polio virus, measles, and Coxsackie virus (e.g., Coxsackie virus A16) .

In cases where the target nucleic acid is a target DNA, the target DNA may be any type of DNA, including types of DNA described elsewhere herein. In some embodiments, the target DNA is viral DNA. In some embodiments, the viral DNA may be pathogenic to the subject. Non-limiting examples of DNA viruses include herpes simplex virus, smallpox, adenovirus (e.g., Adenovirus Type 55, Adenovirus Type 7) and Varicella virus (e.g., chickenpox) .

In some cases, a target DNA may be a bacterial DNA. The bacterial DNA may be from a bacterium pathogenic to the subject. The pathogenic bacterium may be a gram-positive or gram-negative pathogenic bacterium. For example, the pathogenic bacterium may be selected from the group consisting of Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Enterobacter sakazakii, Vibrio Parahemolyticus, Shigella spp., and Mycobacterium tuberculosis (a bacterium known to cause tuberculosis) . In some embodiments, the pathogenic bacterium is Salmonella. In some cases, a target DNA may be a DNA from a pathogenic protozoan, such as, for example one or more protozoans of the Plasmodium type that can cause Malaria.

In any of the various aspects of the present disclosure, a biological sample obtained from a subject is provided with reagents necessary for nucleic acid amplification in a reaction vessel to obtain a reaction mixture. Any suitable reaction vessel may be used. In some embodiments, a reaction vessel comprises a body that can include an interior surface, an exterior surface, an open end, and an opposing closed end. In some embodiments, a reaction vessel may comprise a cap. The cap may be configured to contact the body at its open end, such that when contact is made the open end of the reaction vessel is closed. In some cases, the cap is permanently associated with the reaction vessel such that it remains attached to the reaction vessel in open and closed configurations. In some cases, the cap is removable, such that when the reaction vessel is open, the cap is separated from the reaction vessel. In some embodiments, a reaction vessel may be sealed, in some cases hermetically sealed.

A reaction vessel may be of varied size, shape, weight, and configuration. In some examples, a reaction vessel may be round or oval tubular shaped. In some embodiments, a reaction vessel may be rectangular, square, diamond, circular, elliptical, or triangular shaped. A reaction vessel may be regularly shaped or irregularly shaped. In some embodiments, the closed end of a reaction vessel may have a tapered, rounded, or flat surface. Non-limiting examples of types of a reaction vessel include a tube, a well, a capillary tube, a cartridge, a cuvette, a centrifuge tube, or a pipette tip. Reaction vessels may be constructed of any suitable material with non-limiting examples of such materials that include glasses, metals, plastics, and combinations thereof.

In some embodiments, a reaction vessel is part of an array of reaction vessels. An array of reaction vessels may be particularly useful for automating methods and/or simultaneously processing multiple samples. For example, a reaction vessel may be a well of a microwell plate comprised of a number of wells. In another example, a reaction vessel may be held in a well of a thermal block of a thermocycler, wherein the block of the thermal cycle comprises multiple wells each capable of receiving a sample vessel. An array comprised of reaction vessels may comprise any appropriate number of reaction vessels. For example, an array may comprise at least 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 25, 35, 48, 96, 144, 384, or more reaction vessels. A reaction vessel part of an array of reaction vessels may also be individually addressable by a fluid handling device, such that the fluid handling device can correctly identify a reaction vessel and dispense appropriate fluid materials into the reaction vessel. Fluid handling devices may be useful in automating the addition of fluid materials to reaction vessels.

In some embodiments, a reaction vessel may comprise multiple thermal zones. Thermal zones within a reaction vessel may be achieved by exposing different regions of the reaction vessel to different temperature cycling conditions. For example, a reaction vessel may comprise an upper thermal zone and a lower thermal zone. The upper thermal zone may be capable of a receiving a biological sample and reagents necessary to obtain a reaction mixture for nucleic acid amplification. The reaction mixture can then be subjected to a first thermocycling protocol. After a desired number of cycles, for example, the reaction mixture can slowly, but continuously leak from the upper thermal zone to the lower thermal zone. In the lower thermal zone, the reaction mixture is then subjected to a desired number of cycles of a second thermocycling protocol different from that in the upper thermal zone. Such a strategy may be particularly useful when nested PCR is used to amplify DNA. In some embodiments, thermal zones may be created within a reaction vessel with the aid of thermal sensitive layering materials within the reaction vessels. In such cases, heating of the thermal sensitive layering materials may be used to release reaction mixtures from one thermal zone to the next. In some embodiments, the reaction vessel comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more thermal zones.

In some embodiments, a reaction vessel comprising thermal zones may be used for processing of a biological sample prior to nucleic acid amplification. For example, a lysis agent may be added to a first thermal zone of a reaction vessel prior to adding a biological sample and reagents necessary for nucleic acid amplification. When the biological sample and reagents are added to the reaction vessel comprising the lysis agent, a reaction mixture capable of lysing species (e.g., cells or viral particles) within the biological is obtained. Alternatively, a lysis agent can be added to the first thermal zone of the reaction mixture concurrently with the biological sample and reagents. Subjecting the first thermal zone to temperature conditions suitable for action of the lysis agent may be used to lyse cells and viral particles in the biological sample in the first thermal zone, such that nucleic acids in the biological sample are released into the reaction mixture. After lysis, the reaction mixture can then be permitted to enter a second thermal zone of the reaction vessel for amplification of the released nucleic acid, using amplification methods described herein.

Any type of nucleic acid amplification reaction may be used to amplify a target nucleic acid and generate an amplified product. Moreover, amplification of a nucleic acid may linear, exponential, or a combination thereof. Amplification may be emulsion based or may be non-emulsion based. Non-limiting examples of nucleic acid amplification methods include reverse transcription, primer extension, polymerase chain reaction, ligase chain reaction, helicase-dependent amplification, asymmetric amplification, rolling circle amplification, and multiple displacement amplification (MDA) . In some embodiments, the amplified product may be DNA. In cases where a target RNA is amplified, DNA can be obtained by reverse transcription of the RNA and subsequent amplification of the DNA can be used to generate an amplified DNA product. The amplified DNA product may be indicative of the presence of the target RNA in the biological sample. In cases where DNA is amplified, various DNA amplification protocols may be employed. Non-limiting examples of DNA amplification methods include polymerase chain reaction (PCR) , variants of PCR (e.g., real-time PCR, allele-specific PCR, assembly PCR, asymmetric PCR, digital PCR, emulsion PCR, dial-out PCR, helicase-dependent PCR, nested PCR, hot start PCR, inverse PCR, methylation-specific PCR, miniprimer PCR, multiplex PCR, nested PCR, overlap-extension PCR, thermal asymmetric interlaced PCR, touchdown PCR) , and ligase chain reaction (LCR) . In some cases, DNA amplification is linear. In some cases, DNA amplification is exponential. In some cases, DNA amplification is achieved with nested PCR, which can improve sensitivity of detecting amplified DNA products.

In various aspects, nucleic acid amplification reactions described herein may be conducted in parallel. In general, parallel amplification reactions are amplification reactions that occur in the same reaction vessel and at the same time. Parallel nucleic acid amplification reactions may be conducted, for example, by including reagents necessary for each nucleic acid amplification reaction in a reaction vessel to obtain a reaction mixture and subjecting the reaction mixture to conditions necessary for each nucleic amplification reaction. For example, reverse transcription amplification and DNA amplification may be conducted in parallel, by providing reagents necessary for both amplification methods in a reaction vessel to form to obtain a reaction mixture and subjecting the reaction mixture to conditions suitable for conducting both amplification reactions. DNA generated from reverse transcription of the RNA may be amplified in parallel to generate an amplified DNA product. Any suitable number of nucleic acid amplification reactions may be conducted in parallel. In some cases, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more nucleic acid amplification reactions are conducted in parallel.

An advantage of conducting nucleic acid amplification reactions in parallel can include fast transitions between coupled nucleic acid amplification reactions. For example, a target nucleic acid (e.g., target RNA, target DNA) may be extracted or released from a biological sample during heating phases of parallel nucleic acid amplification. In the case of a target RNA, for example, the biological sample comprising the target RNA can be heated and the target RNA released from the biological sample. The released target RNA can immediately begin reverse transcription (via reverse transcription amplification) to produce complementary DNA. The complementary DNA can then be immediately amplified, often on the order of seconds. Short times between release of a target RNA from a biological sample and reverse transcription of the target RNA to complementary DNA may help minimize the effects of inhibitors in the biological sample that may impede reverse transcription and/or DNA amplification.

In any of the various aspects, primer sets directed to a target nucleic acid may be utilized to conduct nucleic acid amplification reaction. Primer sets generally comprise one or more primers. For example, a primer set may comprise about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more primers. In some cases, a primer set or may comprise primers directed to different amplified products or different nucleic acid amplification reactions. For example, a primer set may comprise a first primer necessary to generate a first strand of nucleic acid product that is complementary to at least a portion of the target nucleic acid and a second primer complementary to the nucleic acid strand product necessary to generate a second strand of nucleic acid product that is complementary to at least a portion of the first strand of nucleic acid product.

For example, a primer set may be directed to a target RNA. The primer set may comprise a first primer that can be used to generate a first strand of nucleic acid product that is complementary to at least a portion the target RNA. In the case of a reverse transcription reaction, the first strand of nucleic acid product may be DNA. The primer set may also comprise a second primer that can be used to generate a second strand of nucleic acid product that is complementary to at least a portion of the first strand of nucleic acid product. In the case of a reverse transcription reaction conducted in parallel with DNA amplification, the second strand of nucleic acid product may be a strand of nucleic acid (e.g., DNA) product that is complementary to a strand of DNA generated from an RNA template.

Where desired, any suitable number of primer sets may be used. For example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more primer sets may be used. Where multiple primer sets are used, one or more primer sets may each correspond to a particular nucleic acid amplification reaction or amplified product.

In some embodiments, a DNA polymerase is used. Any suitable DNA polymerase may be used, including commercially available DNA polymerases. A DNA polymerase generally refers to an enzyme that is capable of incorporating nucleotides to a strand of DNA in a template bound fashion. Non-limiting examples of DNA polymerases include Taq polymerase, Tth polymerase, Tli polymerase, Pfu polymerase, VENT polymerase, DEEPVENT polymerase, EX-Taq polymerase, LA-Taq polymerase, Expand polymerases, Sso polymerase, Poc polymerase, Pab polymerase, Mth polymerase, Pho polymerase, ES4 polymerase, Tru polymerase, Tac polymerase, Tne polymerase, Tma polymerase, Tih polymerase, Tfi polymerase, Platinum Taq polymerases, Hi-Fi polymerase, Tbr polymerase, Tfl polymerase, Pfutubo polymerase, Pyrobest polymerase, Pwo polymerase, KOD polymerase, Bst polymerase, Sac polymerase, Klenow fragment, and variants, modified products and derivatives thereof. For certain Hot Start Polymerase, a denaturation step at 94℃ -95℃ for 2 minutes to 10 minutes may be required, which may change the thermal profile based on different polymerases.

In some embodiments, a reverse transcriptase is used. Any suitable reverse transcriptase may be used. A reverse transcriptase generally refers to an enzyme that is capable of incorporating nucleotides to a strand of DNA, when bound to an RNA template. Non-limiting examples of reverse transcriptases include HIV-1 reverse transcriptase, M-MLV reverse transcriptase, AMV reverse transcriptase, telomerase reverse transcriptase, and variants, modified products and derivatives thereof.

In various aspects, primer extension reactions are utilized to generate amplified product. Primer extension reactions generally comprise a cycle of incubating a reaction mixture at a denaturation temperature for a denaturation duration and incubating a reaction mixture at an elongation temperature for an elongation duration.

Denaturation temperatures may vary depending upon, for example, the particular biological sample analyzed, the particular source of target nucleic acid (e.g., viral particle, bacteria) in the biological sample, the reagents used, and/or the desired reaction conditions. For example, a denaturation temperature may be from about 80℃ to about 110℃. In some examples, a denaturation temperature may be from about 90℃ to about 100℃. In some examples, a denaturation temperature may be from about 90℃ to about 97℃. In some examples, a denaturation temperature may be from about 92℃ to about 95℃. In still other examples, a denaturation temperature may be about 80°, 81℃, 82℃, 83℃, 84℃, 85℃, 86℃, 87℃, 88℃, 89℃, 90℃, 91℃, 92℃, 93℃, 94℃, 95℃, 96℃, 97℃, 98℃, 99℃, or 100℃.

Denaturation durations may vary depending upon, for example, the particular biological sample analyzed, the particular source of target nucleic acid (e.g., viral particle, bacteria) in the biological sample, the reagents used, and/or the desired reaction conditions. For example, a denaturation duration may be less than or equal to 300 seconds, 240 seconds, 180 seconds, 120 seconds, 90 seconds, 60 seconds, 55 seconds, 50 seconds, 45 seconds, 40 seconds, 35 seconds, 30 seconds, 25 seconds, 20 seconds, 15 seconds, 10 seconds, 5 seconds, 2 seconds, or 1 second. For example, a denaturation duration may be no more than 120 seconds, 90 seconds, 60 seconds, 55 seconds, 50 seconds, 45 seconds, 40 seconds, 35 seconds, 30 seconds, 25 seconds, 20 seconds, 15 seconds, 10 seconds, 5 seconds, 2 seconds, or 1 second.

Elongation temperatures may vary depending upon, for example, the particular biological sample analyzed, the particular source of target nucleic acid (e.g., viral particle, bacteria) in the biological sample, the reagents used, and/or the desired reaction conditions. For example, an elongation temperature may be from about 30℃ to about 80℃. In some examples, an elongation temperature may be from about 35℃ to about 72℃. In some examples, an elongation temperature may be from about 45℃ to about 65℃. In some examples, an elongation temperature may be from about 35℃ to about 65℃. In some examples, an elongation temperature may be from about 40℃ to about 60℃. In some examples, an elongation temperature may be from about 50℃ to about 60℃. In still other examples, an elongation temperature may be about 35°, 36℃, 37℃, 38℃, 39℃, 40℃, 41℃, 42℃, 43℃, 44℃, 45℃, 46℃, 47℃, 48℃, 49℃, 50℃, 51℃, 52℃, 53℃, 54℃, 55℃, 56℃, 57℃, 58℃, 59℃, 60℃, 61℃, 62℃, 63℃, 64℃, 65℃, 66℃, 67℃, 68℃, 69℃, 70℃, 71℃, 72℃, 73℃, 74℃, 75℃, 76℃, 77℃, 78℃, 79℃, or 80℃.

Elongation durations may vary depending upon, for example, the particular biological sample analyzed, the particular source of target nucleic acid (e.g., viral particle, bacteria) in the biological sample, the reagents used, and/or the desired reaction conditions. For example, an elongation duration may be less than or equal to 300 seconds, 240 seconds, 180 seconds, 120 seconds, 90 seconds, 60 seconds, 55 seconds, 50 seconds, 45 seconds, 40 seconds, 35 seconds, 30 seconds, 25 seconds, 20 seconds, 15 seconds, 10 seconds, 5 seconds, 2 seconds, or 1 second. For example, an elongation duration may be no more than 120 seconds, 90 seconds, 60 seconds, 55 seconds, 50 seconds, 45 seconds, 40 seconds, 35 seconds, 30 seconds, 25 seconds, 20 seconds, 15 seconds, 10 seconds, 5 seconds, 2 seconds, or 1 second.

In any of the various aspects, multiple cycles of a primer extension reaction can be conducted. Any suitable number of cycles may be conducted. For example, the number of cycles conducted may be less than about 100, 90, 80, 70, 60, 50, 40, 30, 20, 10, or 5 cycles. The number of cycles conducted may depend upon, for example, the number of cycles (e.g., cycle threshold value (Ct) ) necessary to obtain a detectable amplified product (e.g., a detectable amount of amplified DNA product that is indicative of the presence of a target RNA in a biological sample) . For example, the number of cycles necessary to obtain a detectable amplified product (e.g., a detectable amount of DNA product that is indicative of the presence of a target RNA in a biological sample) may be less than about or about 100 cycles, 75 cycles, 70 cycles, 65 cycles, 60 cycles, 55 cycles, 50 cycles, 40 cycles, 35 cycles, 30 cycles, 25 cycles, 20 cycles, 15 cycles, 10 cycles, or 5 cycles. Moreover, in some embodiments, a detectable amount of an amplifiable product (e.g., a detectable amount of DNA product that is indicative of the presence of a target RNA in a biological sample) may be obtained at a cycle threshold value (Ct) of less than 100, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 25, 20, 15, 10, or 5.

The time for which amplification yields a detectable amount of amplified product indicative of the presence of a target nucleic acid amplified can vary depending upon the biological sample from which the target nucleic acid was obtained, the particular nucleic acid amplification reactions to be conducted, and the particular number of cycles of amplification reaction desired. For example, amplification of a target nucleic acid may yield a detectable amount of amplified product indicative to the presence of the target nucleic acid at time period of 120 minutes or less； 90 minutes or less； 60 minutes or less； 50 minutes or less； 45 minutes or less； 40 minutes or less； 35 minutes or less； 30 minutes or less； 25 minutes or less； 20 minutes or less； 15 minutes or less； 10 minutes or less； or 5 minutes or less.

In some embodiments, amplification of a target RNA may yield a detectable amount of amplified DNA product indicative to the presence of the target RNA at time period of 120 minutes or less； 90 minutes or less； 60 minutes or less； 50 minutes or less； 45 minutes or less； 40 minutes or less； 35 minutes or less； 30 minutes or less； 25 minutes or less； 20 minutes or less； 15 minutes or less； 10 minutes or less； or 5 minutes or less.

In some embodiments, a reaction mixture may be subjected to a plurality of series of primer extension reactions. An individual series of the plurality may comprise multiple cycles of a particular primer extension reaction, characterized, for example, by particular denaturation and elongation conditions as described elsewhere herein. Generally, each individual series differs from at least one other individual series in the plurality with respect to, for example, a denaturation condition and/or elongation condition. An individual series may differ from another individual series in a plurality of series, for example, with respect to any one, two, three, or all four of denaturing temperature, denaturing duration, elongation temperature, and elongation duration. Moreover, a plurality of series may comprise any number of individual series such as, for example, at least about or about 2, 3, 4, 5, 6, 7, 8, 9, 10, or more individual series.

For example, a plurality of series of primer extension reactions may comprise a first series and a second series. The first series, for example, may comprise more than ten cycles of a primer extension reaction. Each cycle of the first series may comprise (i) incubating a reaction mixture at about 92℃ to about 95℃ for no more than 30 seconds followed by (ii) incubating the reaction mixture at about 35℃ to about 65℃ for no more than about one minute. The second series, for example, may comprise more than ten cycles of a primer extension reaction. Each cycle of the second series may comprise (i) incubating the reaction mixture at about 92℃ to about 95℃ for no more than 30 seconds followed by (ii) incubating the reaction mixture at about 40℃ to about 60℃ for no more than about 1 minute. In this particular example, the first and second series differ in their elongation temperature condition. The example, however, is not meant to be limiting as any combination of different elongation and denaturing conditions may be used.

In some embodiments, the ramping time (i.e., the time the thermal cycler takes to transition from one temperature to another) and/or ramping rate can be important factors in amplification. For example, the temperature and time for which amplification yields a detectable amount of amplified product indicative of the presence of a target nucleic acid can vary depending upon the ramping rate and/or ramping time. The ramping rate can impact the temperature (s) and time (s) used for amplification.

In some cases, the ramping time and/or ramping rate can be different between cycles. In some situations, however, the ramping time and/or ramping rate between cycles can be the same. The ramping time and/or ramping rate can be adjusted based on the sample (s) that are being processed.

In some situations, the ramping time between different temperatures can be determined, for example, based on the nature of the sample and the reaction conditions. The exact temperature and incubation time can also be determined based on the nature of the sample and the reaction conditions. In some embodiments, a single sample can be processed (e.g., subjected to amplification conditions) multiple times using multiple thermal cycles, with each thermal cycle differing for example by the ramping time, temperature, and/or incubation time. The best or optimum thermal cycle can then be chosen for that particular sample. This provides a robust and efficient method of tailoring the thermal cycles to the specific sample or combination of samples being tested.

In some embodiments, a target nucleic acid may be subjected to a denaturing condition prior to initiation of a primer extension reaction. In the case of a plurality of series of primer extension reactions, the target nucleic acid may be subjected to a denaturing condition prior to executing the plurality of series or may be subjected to a denaturing condition between series of the plurality. For example, the target nucleic acid may be subjected to a denaturing condition between a first series and a second series of a plurality of series. Non-limiting examples of such denaturing conditions include a denaturing temperature profile (e.g., one or more denaturing temperatures) and a denaturing agent.

An advantage of conducting a plurality of series of primer extension reaction may be that, when compared to a single series of primer extension reactions under comparable denaturing and elongation conditions, the plurality of series approach yields a detectable amount of amplified product that is indicative of the presence of a target nucleic acid in a biological sample with a lower cycle threshold value. Use of a plurality of series of primer extension reactions may reduce such cycle threshold values by at least about or about 1％, 5％, 10％, 15％, 20％, 25％, 30％, 35％, 40％, 45％, 50％, 55％, 60％, 65％, 70％, 75％, 80％, 85％, 90％, or 95％when compared to a single series under comparable denaturing and elongation conditions.

In some embodiments, a biological sample may be preheated prior to conducting a primer extension reaction. The temperature (e.g., a preheating temperature) at which and duration (e.g., a preheating duration) for which a biological sample is preheated may vary depending upon, for example, the particular biological sample being analyzed. In some examples, a biological sample may be preheated for no more than about 60 minutes, 50 minutes, 40 minutes, 30 minutes, 25 minutes, 20 minutes, 15 minutes, 10 minutes, 9 minutes, 8 minutes, 7 minutes, 6 minutes, 5 minutes, 4 minutes, 3 minutes, 2 minutes, 1 minute, 45 seconds, 30 seconds, 20 seconds, 15 seconds, 10 seconds, or 5 seconds. In some examples, a biological sample may be preheated at a temperature from about 80℃ to about 110℃. In some examples, a biological sample may be preheated at a temperature from about 90℃ to about 100℃. In some examples, a biological sample may be preheated at a temperature from about 90℃ to about 97℃. In some examples, a biological sample may be preheated at a temperature from about 92℃ to about 95℃. In still other examples, a biological sample may be preheated at a temperature of about 80°, 81℃, 82℃, 83℃, 84℃, 85℃, 86℃, 87℃, 88℃, 89℃, 90℃, 91℃, 92℃, 93℃, 94℃, 95℃, 96℃, 97℃, 98℃, 99℃, or 100℃.

In some embodiments, reagents necessary for conducting nucleic acid amplification, including reagents necessary for conduction of parallel nucleic acid amplification may also include a reporter agent that yields a detectable signal whose presence or absence is indicative of the presence of an amplified product. The intensity of the detectable signal may be proportional to the amount of amplified product. In some cases, where amplified product is generated of a different type of nucleic acid than the target nucleic acid initially amplified, the intensity of the detectable signal may be proportional to the amount of target nucleic acid initially amplified. For example, in the case of amplifying a target RNA via parallel reverse transcription and amplification of the DNA obtained from reverse transcription, reagents necessary for both reactions may also comprise a reporter agent may yield a detectable signal that is indicative of the presence of the amplified DNA product and/or the target RNA amplified. The intensity of the detectable signal may be proportional to the amount of the amplified DNA product and/or the original target RNA amplified. The use of a reporter agent also enables real-time amplification methods, including real-time PCR for DNA amplification.

Reporter agents may be linked with nucleic acids, including amplified products, by covalent or non-covalent interactions. Non-limiting examples of non-covalent interactions include ionic interactions, Van der Waals forces, hydrophobic interactions, hydrogen bonding, and combinations thereof. In some embodiments, reporter agents may bind to initial reactants and changes in reporter agent levels may be used to detect amplified product. In some embodiments, reporter agents may only be detectable (or non-detectable) as nucleic acid amplification progresses. In some embodiments, an optically-active dye (e.g., a fluorescent dye) may be used as may be used as a reporter agent. Non-limiting examples of dyes include SYBR green, SYBR blue, DAPI, propidium iodine, Hoeste, SYBR gold, ethidium bromide, acridines, proflavine, acridine orange, acriflavine, fluorcoumanin, ellipticine, daunomycin, chloroquine, distamycin D, chromomycin, homidium, mithramycin, ruthenium polypyridyls, anthramycin, phenanthridines and acridines, ethidium bromide, propidium iodide, hexidium iodide, dihydroethidium, ethidium homodimer-1 and -2, ethidium monoazide, and ACMA, Hoechst 33258, Hoechst 33342, Hoechst 34580, DAPI, acridine orange, 7-AAD, actinomycin D, LDS751, hydroxystilbamidine, SYTOX Blue, SYTOX Green, SYTOX Orange, POPO-1, POPO-3, YOYO-1, YOYO-3, TOTO-1, TOTO-3, JOJO-1, LOLO-1, BOBO-1, BOBO-3, PO-PRO-1, PO-PRO-3, BO-PRO-1, BO-PRO-3, TO-PRO-1, TO-PRO-3, TO-PRO-5, JO-PRO-1, LO-PRO-1, YO-PRO-1, YO-PRO-3, PicoGreen, OliGreen, RiboGreen, SYBR Gold, SYBR Green I, SYBR Green II, SYBR DX, SYTO-40, -41, -42, -43, -44, -45 (blue) , SYTO-13, -16, -24, -21, -23, -12, -11, -20, -22, -15, -14, -25 (green) , SYTO-81, -80, -82, -83, -84, -85 (orange) , SYTO-64, -17, -59, -61, -62, -60, -63 (red) , fluorescein, fluorescein isothiocyanate (FITC) , tetramethyl rhodamine isothiocyanate (TRITC) , rhodamine, tetramethyl rhodamine, R-phycoerythrin, Cy-2, Cy-3, Cy-3.5, Cy-5, Cy5.5, , Cy-7, Texas Red, Phar-Red, allophycocyanin (APC) , Sybr Green I, Sybr Green II, Sybr Gold, CellTracker Green, 7-AAD, ethidium homodimer I, ethidium homodimer II, ethidium homodimer III, ethidium bromide, umbelliferone, eosin, green fluorescent protein, erythrosin, coumarin, methyl coumarin, pyrene, malachite green, stilbene, lucifer yellow, cascade blue, dichlorotriazinylamine fluorescein, dansyl chloride, fluorescent lanthanide complexes such as those including europium and terbium, carboxy tetrachloro fluorescein, 5 and/or 6-carboxy fluorescein (FAM) , 5- (or 6-) iodoacetamidofluorescein, 5- { [2(and 3) -5- (Acetylmercapto) -succinyl] amino} fluorescein (SAMSA-fluorescein) , lissamine rhodamine B sulfonyl chloride, 5 and/or 6 carboxy rhodamine (ROX) , 7-amino-methyl-coumarin, 7-Amino-4-methylcoumarin-3-acetic acid (AMCA) , BODIPY fluorophores, 8-methoxypyrene-1, 3, 6-trisulfonic acid trisodium salt, 3, 6-Disulfonate-4-amino-naphthalimide, phycobiliproteins, AlexaFluor 350, 405, 430, 488, 532, 546, 555, 568, 594, 610, 633, 635, 647, 660, 680, 700, 750, and 790 dyes, DyLight 350, 405, 488, 550, 594, 633, 650, 680, 755, and 800 dyes, or other fluorophores.

In various aspects, amplified product (e.g., amplified DNA product, amplified RNA product) may be detected. Detection of amplified product, including amplified DNA, may be accomplished with any suitable detection method. The particular type of detection method used may depend, for example, on the particular amplified product, the type of reaction vessel used for amplification, other reagents in a reaction mixture, whether or not a reporter agent was included in a reaction mixture, and if a reporter agent was used, the particular type of reporter agent use. Non-limiting examples of detection methods include optical detection, spectroscopic detection, electrostatic detection, electrochemical detection, and the like. Optical detection methods include, but are not limited to, fluorimetry and UV-vis light absorbance. Spectroscopic detection methods include, but are not limited to, mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, and infrared spectroscopy. Electrostatic detection methods include, but are not limited to, gel based techniques, such as, for example, gel electrophoresis. Electrochemical detection methods include, but are not limited to, electrochemical detection of amplified product after high-performance liquid chromatography separation of the amplified products.

In any of the various aspects, the time required to complete the elements of a method may vary depending upon the particular steps of the method. For example, an amount of time for completing the elements of a method may be from about 5 minutes to about 120 minutes. In other examples, an amount of time for completing the elements of a method may be from about 5 minutes to about 60 minutes. In other examples, an amount of time for completing the elements of a method may be from about 5 minutes to about 30 minutes. In other examples, an amount of time for completing the elements of a method may be less than or equal to 120 minutes, less than or equal to 90 minutes, less than or equal to 75 minutes, less than or equal to 60 minutes, less than or equal to 45 minutes, less than or equal to 40 minutes, less than or equal to 35 minutes, less than or equal to 30 minutes, less than or equal to 25 minutes, less than or equal to 20 minutes, less than or equal to 15 minutes, less than or equal to 10 minutes, or less than or equal to 5 minutes.

In some embodiments, information regarding the presence of and/or an amount of amplified product (e.g., amplified DNA product) may be outputted to a recipient. Information regarding amplified product may be outputted via various approaches. In some embodiments, such information may be provided verbally to a recipient. In some embodiments, such information may be provided in a report. A report may include any number of desired elements, with non-limiting examples that include information regarding the subject (e.g., sex, age, race, health status, etc. ) raw data, processed data (e.g., graphical displays (e.g., figures, charts, data tables, data summaries) , determined cycle threshold values, calculation of starting amount of target polynucleotide) , conclusions about the presence of the target nucleic acid, diagnosis information, prognosis information, disease information, and the like, and combinations thereof. The report may be provided as a printed report (e.g., a hard copy) or may be provided as an electronic report. In some embodiments, including cases where an electronic report is provided, such information may be outputted via an electronic display (e.g., an electronic display screen) , such as a monitor or television, a screen operatively linked with a unit used to obtain the amplified product, a tablet computer screen, a mobile device screen, and the like. Both printed and electronic reports may be stored in files or in databases, respectively, such that they are accessible for comparison with future reports.

Sequencing

In one embodiment, the present disclosure provides for products ready for amplification in preparation for sequencing. In some embodiments, the target polynucleotides are pooled followed by sequencing one or more polynucleotides in the pool. Sequencing methods utilizing adaptor incorporated sequences may be as described, for example, in U.S. Patent Nos. 8,053,192 and 8, 017, 335, each of which is entirely incorporated herein by reference.

Sequencing processes are generally template dependent. Nucleic acid sequence analysis that employs template dependent synthesis identifies individual bases, or groups of bases as they are added during a template mediated synthesis reaction, such as a primer extension reaction, where the identity of the base is complementary to the template sequence to which the primer sequence is hybridized during synthesis. Other such processes include ligation driven processes, where oligonucleotides or polynucleotides are complexed with an underlying template sequence, in order to identify the sequence of nucleotides in that sequence. Typically, such processes are enzymatically mediated using nucleic acid polymerases, such as DNA polymerases, RNA polymerases, reverse transcriptases, and the like, or other enzymes such as in the case of ligation driven processes, e.g., ligases.

Sequence analysis using template dependent synthesis can include a number of different processes. For example, in the ubiquitously practiced four-color Sanger sequencing methods, a population of template molecules is used to create a population of complementary fragment sequences. Primer extension is carried out in the presence of the four naturally occurring nucleotides, and with a sub-population of dye labeled terminator nucleotides, e.g., dideoxyribonucleotides, where each type of terminator (ddATP, ddGTP, ddTTP, ddCTP) includes a different detectable label. As a result, a nested set of fragments is created where the fragments terminate at each nucleotide in the sequence beyond the primer, and are labeled in a manner that permits identification of the terminating nucleotide. The nested fragment population is then subjected to size based separation, e.g., using capillary electrophoresis, and the labels associated with each different sized fragment is identified to identify the terminating nucleotide. As a result, the sequence of labels moving past a detector in the separation system provides a direct readout of the sequence information of the synthesized fragments, and by complementarity, the underlying template (See, e.g., U.S. Pat. No. 5,171,534, incorporated herein by reference in its entirety for all purposes) .

Other examples of template dependent sequencing methods include sequence by synthesis processes, where individual nucleotides are identified iteratively, as they are added to the growing primer extension product.

Pyrosequencing is an example of a sequence by synthesis process that identifies the incorporation of a nucleotide by assaying the resulting synthesis mixture for the presence of by-products of the sequencing reaction, namely pyrophosphate. In particular, a primer/template/polymerase complex is contacted with a single type of nucleotide. If that nucleotide is incorporated, the polymerization reaction cleaves the nucleoside triphosphate between the α and β phosphates of the triphosphate chain, releasing pyrophosphate. The presence of released pyrophosphate is then identified using a chemiluminescent enzyme reporter system that converts the pyrophosphate, with AMP, into ATP, then measures ATP using a luciferase enzyme to produce measurable light signals. In some cases, if light is detected, the base is incorporated, if no light is detected, the base is not incorporated. Following appropriate washing steps, the various bases are cyclically contacted with the complex to sequentially identify subsequent bases in the template sequence. See, e.g., U.S. Pat. No. 6,210,891, incorporated herein by reference in its entirety for all purposes) .

In related processes, the primer/template/polymerase complex is immobilized upon a substrate and the complex is contacted with labeled nucleotides. The immobilization of the complex may be through the primer sequence, the template sequence and/or the polymerase enzyme, and may be covalent or noncovalent. For example, immobilization of the complex can be via a linkage between the polymerase or the primer and the substrate surface. A variety of types of linkages are useful for this attachment, including, e.g., provision of biotinylated surface components, using e.g., biotin-PEG-silane linkage chemistries, followed by biotinylation of the molecule to be immobilized, and subsequent linkage through, e.g., a streptavidin bridge. Other synthetic coupling chemistries, as well as non-specific protein adsorption can also be employed for immobilization. In alternate configurations, the nucleotides are provided with and without removable terminator groups. Upon incorporation, the label is coupled with the complex and is thus detectable. In the case of terminator bearing nucleotides, all four different nucleotides, bearing individually identifiable labels, are contacted with the complex. Incorporation of the labeled nucleotide arrests extension, by virtue of the presence of the terminator, and adds the label to the complex. The label and terminator are then removed from the incorporated nucleotide, and following appropriate washing steps, the process is repeated. In the case of non-terminated nucleotides, a single type of labeled nucleotide is added to the complex to determine whether it will be incorporated, as with pyrosequencing. Following removal of the label group on the nucleotide and appropriate washing steps, the various different nucleotides are cycled through the reaction mixture in the same process. See, e.g., U.S. Pat. No. 6,833,246, incorporated herein by reference in its entirety for all purposes) . For example, the Illumina Genome Analyzer System is based on technology described in WO 98/44151, hereby incorporated by reference, wherein DNA molecules are bound to a sequencing platform (flow cell) via an anchor probe binding site (otherwise referred to as a flow cell binding site) and amplified in situ on a glass slide. The DNA molecules are then annealed to a sequencing primer and sequenced in parallel base-by-base using a reversible terminator approach. Typically, the Illumina Genome Analyzer System utilizes flow-cells with 8 channels, generating sequencing reads of 18 to 36 bases in length, generating >1.3 Gbp of high quality data per run. Accordingly, the methods of the invention are useful for sequencing by the method commercialized by Illumina, as described U.S. Pat. Nos. 5,750,341； 6,306,597； and 5,969,119, each of which is entirely incorporated herein by reference. Directional (strand-specific) cDNA libraries are prepared using the methods of the present invention, and the selected single-stranded nucleic acid is amplified, for example, by PCR. The resulting nucleic acid is then denatured and the single-stranded amplified polynucleotides are randomly attached to the inside surface of flow-cell channels. Unlabeled nucleotides are added to initiate solid-phase bridge amplification to produce dense clusters of double-stranded DNA. To initiate the first base sequencing cycle, four labeled reversible terminators, primers, and DNA polymerase are added. After laser excitation, fluorescence from each cluster on the flow cell is imaged. The identity of the first base for each cluster is then recorded. Cycles of sequencing are performed to determine the fragment sequence one base at a time.

In yet a further sequence by synthesis process, the incorporation of differently labeled nucleotides is observed in real time as template dependent synthesis is carried out. In particular, an individual immobilized primer/template/polymerase complex is observed as fluorescently labeled nucleotides are incorporated, permitting real time identification of each added base as it is added. In this process, label groups are attached to a portion of the nucleotide that is cleaved during incorporation. For example, by attaching the label group to a portion of the phosphate chain removed during incorporation, i.e., a β, γ, or other terminal phosphate group on a nucleoside polyphosphate, the label is not incorporated into the nascent strand, and instead, natural DNA is produced. Observation of individual molecules typically involves the optical confinement of the complex within a very small illumination volume. By optically confining the complex, one creates a monitored region in which randomly diffusing nucleotides are present for a very short period of time, while incorporated nucleotides are retained within the observation volume for longer as they are being incorporated. This results in a characteristic signal associated with the incorporation event, which is also characterized by a signal profile that is characteristic of the base being added. In related aspects, interacting label components, such as fluorescent resonant energy transfer (FRET) dye pairs, are provided upon the polymerase or other portion of the complex and the incorporating nucleotide, such that the incorporation event puts the labeling components in interactive proximity, and a characteristic signal results, that is again, also characteristic of the base being incorporated (See, e.g., U.S. Pat. Nos. 6,056,661, 6,917,726, 7,033,764, 7,052,847, 7,056,676, 7,170,050, 7,361,466, 7,416,844 and Published U.S. Patent Application No. 2007-0134128, the full disclosures of which are hereby incorporated herein by reference in their entirety for all purposes) .

In some embodiments, the nucleic acids in the sample can be sequenced by ligation. This method uses a DNA ligase enzyme to identify the target sequence, for example, as used in the polony method and in the SOLiD technology (Applied Biosystems, now Invitrogen) . In general, a pool of all possible oligonucleotides of a fixed length is provided, labeled according to the sequenced position. Oligonucleotides are annealed and ligated； the preferential ligation by DNA ligase for matching sequences results in a signal corresponding to the complementary sequence at that position.

Thus, in some embodiments, the methods of the invention are useful for preparing target polynucleotides for sequencing by the sequencing by ligation methods commercialized by Applied Biosystems (e.g., SOLiD sequencing) . In other embodiments, the methods are useful for preparing target polynucleotides for sequencing by synthesis using the methods commercialized by 454/Roche Life Sciences, including but not limited to the methods and apparatus described in Margulies et al., Nature (2005) 437: 376-380 (2005) ； and U.S. Pat. Nos. 7,244,559； 7,335,762； 7,211,390； 7,244,567； 7,264,929； and 7,323,305, each of which is entirely incorporated herein by reference. In other embodiments, the methods are useful for preparing target polynucleotide (s) for sequencing by the methods commercialized by Helicos BioSciences Corporation (Cambridge, Mass. ) as described in U.S. application Ser. No. 11/167,046, and U.S. Pat. Nos. 7,501,245； 7,491,498； 7,276,720； and in U.S. Patent Application Publication Nos. US20090061439； US20080087826； US20060286566； US20060024711； US20060024678； US20080213770； and US20080103058, each of which is entirely incorporated herein by reference. In other embodiments, the methods are useful for preparing target polynucleotide (s) for sequencing by the methods commercialized by Pacific Biosciences as described in U.S. Pat. Nos. 7,462,452； 7,476,504； 7,405,281； 7,170,050； 7,462,468； 7,476,503； 7,315,019； 7,302,146； 7,313,308； and US Application Publication Nos. US20090029385； US20090068655； US20090024331； and US20080206764, each of which is entirely incorporated herein by reference. In general, double stranded fragment polynucleotides can be prepared by the methods of the present invention. The polynucleotides can then be immobilized in zero mode waveguide arrays. The methods may include a step of rendering the nucleic acid bound to the waveguide arrays single stranded or partially single stranded. Polymerase and labeled nucleotides are added in a reaction mixture, and nucleotide incorporations are visualized via fluorescent labels attached to the terminal phosphate groups of the nucleotides. The fluorescent labels are clipped off as part of the nucleotide incorporation. In some cases, circular templates are utilized to enable multiple reads on a single molecule.

Another example of a sequencing technique that can be used in the methods of the provided invention is nanopore sequencing (see e.g. Soni G V and Meller A. (2007) Clin Chem 53: 1996-2001) . A nanopore can be a small hole of the order of 1 nanometer in diameter. Immersion of a nanopore in a conducting fluid and application of a potential across it can result in a slight electrical current due to conduction of ions through the nanopore. The amount of current that flows is sensitive to the size of the nanopore. As a DNA molecule passes through a nanopore, each nucleotide on the DNA molecule obstructs the nanopore to a different degree. Thus, the change in the current passing through the nanopore as the DNA molecule passes through the nanopore can represent a reading of the DNA sequence.

Another example of a sequencing technique that can be used in the methods of the provided invention is semiconductor sequencing provided by Ion Torrent (e.g., using the Ion Personal Genome Machine (PGM) ) . Ion Torrent technology can use a semiconductor chip with multiple layers, e.g., a layer with micro-machined wells, an ion-sensitive layer, and an ion sensor layer. Nucleic acids can be introduced into the wells, e.g., a clonal population of single nucleic can be attached to a single bead, and the bead can be introduced into a well. To initiate sequencing of the nucleic acids on the beads, one type of deoxyribonucleotide (e.g., dATP, dCTP, dGTP, or dTTP) can be introduced into the wells. When one or more nucleotides are incorporated by DNA polymerase, protons (hydrogen ions) are released in the well, which can be detected by the ion sensor. The semiconductor chip can then be washed and the process can be repeated with a different deoxyribonucleotide. A plurality of nucleic acids can be sequenced in the wells of a semiconductor chip. The semiconductor chip can comprise chemical-sensitive field effect transistor (chemFET) arrays to sequence DNA (for example, as described in U.S. Patent Application Publication No. 20090026082, which is entirely incorporated herein by reference) . Incorporation of one or more triphosphates into a new nucleic acid strand at the 3′end of the sequencing primer can be detected by a change in current by a chemFET. An array can have multiple chemFET sensors.

In some embodiments, the methods are useful for preparing target polynucleotide (s) from selectively enriched populations of specific sequence regions of interest in a strand-specific manner for sequencing by the methods described below or elsewhere herein.

For example the methods are useful for sequencing by the method commercialized by Illumina as described U.S. Pat. Nos. 5,750,341； 6,306,597； and 5,969,119, each of which is entirely incorporated herein by reference. In general, double stranded fragment polynucleotides can be prepared by the methods of the present invention to produce amplified nucleic acid sequences tagged at one (e.g., (A) / (A′) or both ends (e.g., (A) / (A′) and (C) / (C′) ) . In some cases, single stranded nucleic acid tagged at one or both ends is amplified by the methods of the present invention (e.g., by SPIA or linear PCR) . The resulting nucleic acid is then denatured and the single stranded amplified polynucleotides are randomly attached to the inside surface of flow-cell channels. Unlabeled nucleotides are added to initiate solid-phase bridge amplification to produce dense clusters of double-stranded DNA. To initiate the first base sequencing cycle, four labeled reversible terminators, primers, and DNA polymerase are added. After laser excitation, fluorescence from each cluster on the flow cell is imaged. The identity of the first base for each cluster is then recorded. Cycles of sequencing are performed to determine the fragment sequence one base at a time. For paired-end sequencing, such as for example, when the polynucleotides are labeled at both ends by the methods of the present invention, sequencing templates can be regenerated in-situ so that the opposite end of the fragment can also be sequenced.

Detectors

A detector of the device can detect a signal during a nucleic acid amplification reaction. The detector can detect the signal without removing the sample from the device. In various aspects, the detector can detect amplified product (e.g., amplified DNA product, amplified RNA product) . Detection of amplified product, including amplified DNA, can be accomplished with any suitable detection method. The particular type of detection method used can depend, for example, on the particular amplified product, the type of reaction vessel used for amplification, other reagents in a reaction mixture, whether or not a reporter agent was included in a reaction mixture, and if a reporter agent was used, the particular type of reporter agent use. Non-limiting examples of detection methods include optical detection, spectroscopic detection, electrostatic detection, and electrochemical detection. Optical detection methods include, but are not limited to, fluorimetry and UV-vis light absorbance. Spectroscopic detection methods include, but are not limited to, mass spectrometry, nuclear magnetic resonance (NMR) spectroscopy, and infrared spectroscopy. Electrostatic detection methods include but are not limited to gel based techniques, such as, for example, gel electrophoresis. Electrochemical detection methods include, but are not limited to, electrochemical detection of amplified product after high-performance liquid chromatography separation of the amplified products.

The detector can be mounted on a moveable element, such as those described in this disclosure. The detector can be driven by a separate drive motor or can be driven by a motor, belt, or other driving element shared with other moveable elements.

The detector can comprise an image sensor or image sensors. The image sensor can be capable of optical detection. The image sensor can comprise a charge-coupled device (CCD) sensor, including a cooled CCD. The image sensor can comprise an active-pixel sensor (APS) , such as a CMOS or NMOS sensor. The detector can comprise a laser sensor. The detector can comprise a photodiode, such as an avalanche photodiode. The detector can comprise a photomultiplier tube (PMT) . The sensors can comprise a single sensor or multiple sensors, of the same type or of different types.

The detector can detect an optical signal from the sample. The optical signal can be a fluorescent or other luminescent signal from the sample. The optical signal can be generated by the sample in response to a stimulation light provided to the sample. Stimulation light can be provided by a light source. The light source can comprise a lamp, such as an incandescent, halogen, fluorescent, gas-discharge, arc, or LED lamp. The light source can comprise a laser. The light source can produce a specific wavelength or range or wavelengths, such as UV. The light source can comprise filters for controlling the output wavelength or wavelengths. The light source can comprise multiple light sources, of the same or of different types, which can be used separately or in combination. The light source can be within the device. In some instances, light can be absorbed by the sample, and the sample can emit light. The emitted light can be at the same or different wavelength from the emitted light. In some instances, the optical signal can be a reflection of light from the light source. Alternatively, light can be shined through the sample, and the detector can be capable of detecting the light that passes through the sample.

An optical path can be provided between the sample and the detector. A signal from the sample can reach the detector via the optical path. An optical signal from a sample can traverse the optical path to reach the detector. The optical path can include direct line-of-sight between the sample and the detector. In some instances, one or more optical elements can be provided between the sample and the detector. Examples of optical elements can include lenses, mirrors, prisms, diffusers, concentrators, filters, dichroics, optical fibers, or any other type of optical elements. The optical path may be provided entirely within a housing of the device. The housing can optically isolate the optical path from the surrounding environment. For example, the housing can be light-tight so that little or no interfering optical signals can be provided within the housing that can interfere with the optical path. Light from outside the housing can be blocked from entering the interior of the housing. This can advantageously reduce inaccuracies in the optical signal detected by the detector. The optical path can remain while the nucleic acid amplification is occurring. The detector can be able to continuously or periodically detect signals from the ample while the nucleic acid amplification is occurring via the optical path.

In some embodiments, information regarding the presence of and/or an amount of amplified product (e.g., amplified DNA product) can be outputted to a recipient. Information regarding amplified product can be outputted via any suitable approach. Such information can be provided in real-time while the nucleic-acid amplification is underway. In other instances, the information can be provided once the nucleic acid amplification has been completed. In some instances, some data can be provided in real-time while other data can be presented once the amplification is completed.

In some embodiments, such information can be provided verbally to a recipient. In some embodiments, such information can be provided in a report. A report can include any number of desired elements, with non-limiting examples that include information regarding the subject (e.g., sex, age, race, health status, etc. ) raw data, processed data (e.g. graphical displays (e.g., figures, charts, data tables, data summaries) , determined cycle threshold values, calculation of starting amount of target polynucleotide) , conclusions about the presence of the target nucleic acid, diagnosis information, prognosis information, disease information, and the like, and combinations thereof. The report can be provided as a printed report (e.g., a hard copy) or can be provided as an electronic report. In some embodiments, including cases where an electronic report is provided, such information can be outputted via an electronic display, such as a monitor or television, a screen operatively linked with a unit used to obtain the amplified product, a tablet computer screen, a mobile device screen, and the like. Both printed and electronic reports can be stored in files or in databases, respectively, such that they are accessible for comparison with future reports.

Computer control systems

The present disclosure provides computer control systems that are programmed to implement methods of the disclosure. FIG. 30 shows a computer system 1101 that is programmed or otherwise configured to collect, process, and/or analyze a biological sample as described herein. The computer system 1101 can regulate various aspects of the system and/or the method of the present disclosure, such as, for example, collection, processing, and/or analysis of a biological sample. The computer system 1101 can be an electronic device of a user or a computer system that is remotely located with respect to the electronic device. The electronic device can be a mobile electronic device.

The computer system 1101 includes a central processing unit (CPU, also “processor” and “computer processor” herein) 1105, which can be a single core or multi core processor, or a plurality of processors for parallel processing. The computer system 1101 also includes memory or memory location 1110 (e.g., random-access memory, read-only memory, flash memory) , electronic storage unit 1115 (e.g., hard disk) , communication interface 1120 (e.g., network adapter) for communicating with one or more other systems, and peripheral devices 1125, such as cache, other memory, data storage and/or electronic display adapters. The memory 1110, storage unit 1115, interface 1120 and peripheral devices 1125 are in communication with the CPU 1105 through a communication bus (solid lines) , such as a motherboard. The storage unit 1115 can be a data storage unit (or data repository) for storing data. The computer system 1101 can be operatively coupled to a computer network ( “network” ) 1130 with the aid of the communication interface 1120. The network 1130 can be the Internet, an internet and/or extranet, or an intranet and/or extranet that is in communication with the Internet. The network 1130 in some cases is a telecommunication and/or data network. The network 1130 can include one or more computer servers, which can enable distributed computing, such as cloud computing. The network 1130, in some cases with the aid of the computer system 1101, can implement a peer-to-peer network, which may enable devices coupled to the computer system 1101 to behave as a client or a server.

The CPU 1105 can execute a sequence of machine-readable instructions, which can be embodied in a program or software. The instructions may be stored in a memory location, such as the memory 1110. The instructions can be directed to the CPU 1105, which can subsequently program or otherwise configure the CPU 1105 to implement methods of the present disclosure. Examples of operations performed by the CPU 1105 can include fetch, decode, execute, and writeback.

The CPU 1105 can be part of a circuit, such as an integrated circuit. One or more other components of the system 1101 can be included in the circuit. In some cases, the circuit is an application specific integrated circuit (ASIC) .

The storage unit 1115 can store files, such as drivers, libraries and saved programs. The storage unit 1115 can store user data, e.g., user preferences and user programs. The computer system 1101 in some cases can include one or more additional data storage units that are external to the computer system 1101, such as located on a remote server that is in communication with the computer system 1101 through an intranet or the Internet.

The computer system 1101 can communicate with one or more remote computer systems through the network 1130. For instance, the computer system 1101 can communicate with a remote computer system of a user (e.g., a subject, or a healthcare professional) . Examples of remote computer systems include personal computers (e.g., portable PC) , slate or tablet PC’s (e.g.,

iPad,

Galaxy Tab) , telephones, Smart phones (e.g.,

iPhone, Android-enabled device,

) , or personal digital assistants. The user can access the computer system 1101 via the network 1130.

Methods as described herein can be implemented by way of machine (e.g., computer processor) executable code stored on an electronic storage location of the computer system 1101, such as, for example, on the memory 1110 or electronic storage unit 1115. The machine executable or machine readable code can be provided in the form of software. During use, the code can be executed by the processor 1105. In some cases, the code can be retrieved from the storage unit 1115 and stored on the memory 1110 for ready access by the processor 1105. In some situations, the electronic storage unit 1115 can be precluded, and machine-executable instructions are stored on memory 1110.

The code can be pre-compiled and configured for use with a machine having a processer adapted to execute the code, or can be compiled during runtime. The code can be supplied in a programming language that can be selected to enable the code to execute in a pre-compiled or as-compiled fashion.

Aspects of the systems and methods provided herein, such as the computer system 1101, can be embodied in programming. Various aspects of the technology may be thought of as “products” or “articles of manufacture” typically in the form of machine (or processor) executable code and/or associated data that is carried on or embodied in a type of machine readable medium. Machine-executable code can be stored on an electronic storage unit, such as memory (e.g., read-only memory, random-access memory, flash memory) or a hard disk. “Storage” type media can include any or all of the tangible memory of the computers, processors or the like, or associated modules thereof, such as various semiconductor memories, tape drives, disk drives and the like, which may provide non-transitory storage at any time for the software programming. All or portions of the software may at times be communicated through the Internet or various other telecommunication networks. Such communications, for example, may enable loading of the software from one computer or processor into another, for example, from a management server or host computer into the computer platform of an application server. Thus, another type of media that may bear the software elements includes optical, electrical and electromagnetic waves, such as used across physical interfaces between local devices, through wired and optical landline networks and over various air-links. The physical elements that carry such waves, such as wired or wireless links, optical links or the like, also may be considered as media bearing the software. As used herein, unless restricted to non-transitory, tangible “storage” media, terms such as computer or machine “readable medium” refer to any medium that participates in providing instructions to a processor for execution.

Hence, a machine readable medium, such as computer-executable code, may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non-volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computer (s) or the like, such as may be used to implement the databases, etc. shown in the drawings. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables； copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD-ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution.

The computer system 1101 can include or be in communication with an electronic display 1135 that comprises a user interface (UI) 1140 for providing, for example, instructions and options as to the collection, processing, and/or analysis of a biological samples. Examples of UI’s include, without limitation, a graphical user interface (GUI) and web-based user interface.

Methods and systems of the present disclosure can be implemented by way of one or more algorithms. An algorithm can be implemented by way of software upon execution by the central processing unit 1105. The algorithm can, for example, implement the methods of the present disclosure, including the collection, processing, and/or analysis of a biological samples.

EXAMPLES

Example 1: Integrated sample collection, processing, and analysis system

Fig. 13A-F represent an exemplary integrated sample collection, processing and analysis system comprising an electronic device 201, a dispensing unit 203, and a sample processing unit 204 in a front view (Fig. 13A) , an top view (Fig. 13B) , a back view (Fig. 13C) , a right view (Fig. 13D) , a left view (Fig. 13E) , and a top right three quarter view (Fig. 13F) .

The electronic device 201, the dispensing unit 203, and the sample processing unit 204 may be connected via one or more communication interfaces (not shown) .

An alternative configuration of the integrated system involves the combination of the electronic device 201 in communication with the dispensing unit 203. This integrated system is capable of dispensing commodities stored in the dispensing unit, but not sample processing (Fig. 14) .

Another alternative configuration of the integrated system involves the combination of the electronic device 201 in communication with the sample processing unit 204 which is also capable of dispensing commodities (Fig. 14) .

Fig. 15 is the front view of an exemplary electronic device 201 in accordance with the present disclosure. On the front panel are disposed a display screen 2011, buttons 2012, a cash port 2013, a card insert 2014, a printout port 2015, and a fingerprint recognition area 2016.

Fig. 16 is a top right three quarter view of a portion of the dispensing unit 203. Commodities such as sample collections units are displayed in the commodity display window 2031 which allows a user to view and select. The dispensing unit 203 further comprises several commodity selection levers 2035 above the commodity dispensing port 2032 for selecting and releasing commodities. The user may push the commodity selection lever 2035 in one direction, for example, up, to select the commodity for dispensing. In some cases, the dispensing unit displays a visual signal indicating the selected commodity, such as flashing light close to the displayed commodity. In some cases, with the lever pushed one step up, the visual signal indicating the selected commodity moves from one commodity to the next, allowing the user to control which commodity to select.

Upon selection of the commodity to be dispensed, the user may push the commodity selection lever 2035 in the opposite direction, for example, all the way down, to effect the dispensing unit 203 to dispense the selected commodity 209 from the commodity dispensing port 2032. The user may then pick up the commodity 209, in some cases a sample collection unit or a kit as described herein.

In some examples, the dispensing unit 203 does not allow the dispensing of the commodity 209 even with pushing of the commodity selection lever 2035 as described above unless the user has authenticated himself/herself and/or paid via the electronic device 201.

Alternatively, the user may directly enter the commodity to be dispensed via the electronic device 201, which upon authentication of and/or payment by the user, autonomously selects the commodity to be dispensed and releases it through the commodity dispensing port 2032 for the user to pick up.

Fig. 17A-B represents an exemplary sample processing unit 204 of the present disclosure in the front view (Fig. 17A) and the top right three quarter view (Fig. 17B) . The sample processing unit 204 may also include a sample dispensing unit in the same housing. As viewed from the front side of the sample processing unit 204, it comprises several commodity dispensing ports 2101, several storages for commodities 2103, a sample receiving port 2111, a barcode scanner, several ventilation ports 2041, several exterior UV lamp 2042, a detector 2043, a shaft 2044, several interior UV lamp 2045, and a reactant swing arm 2126.

The exterior UV lamps 2042 allow sterilization of the area around the sample receiving port and the commodity dispensing ports. The interior UV lamps 2045 allow sterilization of the various storage areas within the housing of the sample processing unit.

The ventilation ports 2041 allows air to be blown out from the sample processing unit 204 to clear any dust or other particles deposited around the sample receiving port 2111 and/or the commodity dispensing ports 2101.

Fig. 18A-D represent the sample processing unit 204 with the back of its housing swung out almost 90 degree in the front top right three quarter view (Fig. 18A) , the back top right three quarter view (Fig. 18B) , the right view (Fig. 18C) and the back view (Fig. 18D) , to expose the interior structure of it. As viewed from different perspectives in Fig. 18A-D, the sample processing unit 204 further comprises a storage for reactant 2123, a storage for undetected samples 2133, a storage for detected samples 2143, a fridging system 2047, a sample swing arm 2136, a sample recovering rod 2145, a commodity dispensing rod 2105, a reactant swing arm 2126, and the detector 2043.

Fig. 19 depicts the process of dispensing a commodity, such as a sample collection unit or kit as described herein. A shutter 2109 is usually deployed in a closed position, preventing access to the commodity dispensing port 2101. When the sample processing unit 204 is effected to dispense the commodity, the shutter 2109 is effected to be deployed in an open position, allowing access to the commodity dispensing port 2101. Meanwhile, a lid which usually covers the commodity dispensing port 2101, if present, slides away from the commodity dispensing port 2101, leaving the port open. Then, the commodity dispensing rod 2105, together with the commodity 210 docking on the upper end of the rod, moves along its axial direction through the commodity dispensing port 2101, presenting the commodity 210 to the user. The user may then pick up the commodity 210.

If the commodity 210 that the user receives is a sample collection unit or a kit comprising a sample collection unit, the user may take a sample and put it in the sample collection unit for recovery and processing by the sample processing unit 204.

Fig. 20-25 depicts the process by which the sample processing unit 204 receives, stores, and analyzes the collected sample. As depicted in Fig. 20, a shutter 2119 is usually deployed in a closed position, preventing access to the sample receiving port 2111. When the sample processing unit 204 is effected to receive the collected sample, the shutter 2119 is effected to be deployed in an open position, allowing access to the sample receiving port 2111. Meanwhile, a lid which usually covers the sample receiving port 2111, if present, slides away from the sample receiving port 2111, leaving the port open. Then, the sample receiving rod 2115 moves along its axial direction through the sample receiving port 2111, presenting a docking position on the upper end of the sample receiving rod 2115 to the user. The user may then dock the sample collection unit 211 with collected sample in it to the upper end of the sample receiving rod 2115. Meanwhile, a barcode scanner 2112 can scan any barcode on the sample collection unit 211 for, for example, authentication, extraction of assay information from the unit, and/or informing the sample processing unit 204 that the collected sample has been docked.

In Fig. 21, a reactant dispensing rod 2125 moves along its axial direction downwards to bring a reactant vessel 212 to the reactant swing arm 2126 (see left panel) . The reactant swing arm 2126 then swings out for about 90 degree as shown in the right panel.

As can be seen in Fig. 22, swinging out of the reactant swing arm 2126 brings the reactant vessel 212 docked on the swing arm in axial with and directly above the received sample collection unit 211 (see left panel) . Then, the sample receiving rod 2115, with the sample collection unit 211 docked on the upper end of the rod, moves along its axial direction towards the reactant vessel 212 until the sample collection unit 211 engages the reactant vessel 212. In some cases, the engagement of the sample collection unit 211 and the reactant vessel 212 allows the sample collection unit 211 to undock from the sample receiving rod 2115 and be detachably fastened to the reactant vessel 212 (see right panel) .

As can be seen in Fig. 23, after the sample collection unit 211 and the reactant vessel 212 are detachably fastened to each other, the sample receiving rod 2115 retracts to its original position (see upper left panel) . Then, the reactant swing arm 2126, with both the reactant vessel 212 and the sample collection unit 212 docked thereupon, swing to the storage for undetected samples 2133 and unload both the reaction vessel 212 and the sample collection unit 211 (see upper right panel) . The reactant swing arm 2126 then reverts to its original position.

Moreover, after the sample collection unit 211 and the reactant vessel 212 are detachably fastened to each other, mixing of the reactant and the collected sample may occur. In some cases, the collected sample has already been mixed with a buffer before received by the sample processing unit 204, as described in Example 2-5. The mixing of the reactant and the collected sample may occur immediately after the detachably fastening between the sample collection unit 211 and the reactant vessel 212. Alternatively, the mixing may occur immediately prior to the detection of the sample as described below. Alternatively, the mixing may occur any time between the aforesaid two time points.

A plurality of combined reactant vessel/sample collection units 213 are thus stacked in the storage for undetected samples 2113, as shown in Fig. 24. The storage comprises two decks. The combined reactant vessel/sample collection units 213 may be transported from the upper deck where they are originally deposited to the lower deck from which they can be brought to detection as depicted in Fig. 25.

Fig. 25 depicts the process by which the combined reactant vessel/sample collection unit 213 is brought to detection. The sample swing arm 2136 swings to the lower deck of the storage for undetected samples 2136 and picks up the combined reactant vessel/sample collection unit 213 (upper left panel and upper right panel) . The sample swing arm 2136 then swings out to a detection position where detection of the sample may occur (lower left panel) . After detection, the sample swing arm 2136 may revert to its original position, where the combined reactant vessel/sample collection unit 213 (now becomes the detected sample 214) is in axial and directly above the sample recovering rod 2145 as depicted in Fig. 26.

Fig. 26 depicts the process by which the detected sample 214 is recovered. The sample recovering rod 2145 moves along its axial direction towards the detected sample 214 until the latter docks on the upper end of the sample recovering rod 2145 (the upper panels) . The sample recovering rod 2145 then retracts back into the storage for detected samples 2143, along with the detected sample 214 (the lower panels) . Once in the storage for detected samples 2143, the detected sample 214 can now be unloaded from the sample recovering rod 2145 (not shown) .

Example 2: Sample collection unit for solid samples

Fig. 27A-G depict a sample collection unit for solid that can be used for the system and/or method of the present disclosure.

The sample collection unit for solid comprises a collection vessel 1501, a buffer reservoir 1502 with buffer 1504 contained therein, a cap 1503, and a piercing member 1505, as depicted in Fig. 27A. The buffer reservoir 1502 is integral to or detachably fastened to the cap 1503. Moreover, the buffer reservoir 1502 is in a first position relative to the collection vessel 1501 that it is cleared off from the piercing member 1505.

Before use, the cap 1503, together with the buffer reservoir 1502 as well as buffer 1504, is removed from the collection vessel 1501, as depicted in Fig. 27B. Subsequently, the piercing member 1505 is also removed from the collection vessel 1501 (Fig. 27C) . A solid sample 1509 is then put into the collection vessel 1501 (Fig. 27D) .

Subsequently, the piercing member 1505 (Fig. 27E) and the cap 1503, together with the buffer reservoir as well as buffer 1502 (Fig. 27F) are put back to the collection vessel 1501 such that the buffer reservoir 1502 remains in the first position relative to the collection vessel 1501.

Finally, the cap 1503 is further pressed downward against the collection vessel 1501, which brings the buffer reservoir 1502 to a second position relative to the collection vessel 1502 where the bottom of the buffer reservoir 1502 is pressed against the piercing member 1505. The piercing member 1505 has a plurality of solid needles deposited thereon which pierce through the bottom of the buffer reservoir 1502, allowing buffer 1504 to flow into the collection vessel and mix with the solid sample 1509, as depicted in Fig. 27G.

The sample collection unit, together with the collected solid sample 1509, may be used in the system and/or method of the present disclosure. In some cases, the sample collection unit may be subjected to the sample processing and analysis procedure as described in Example 1.

Example 3: Sample collection unit for liquid samples

Fig. 28A-G depict a sample collection unit for liquid that can be used for the system and/or method of the present disclosure.

The sample collection unit for liquid comprises a collection vessel 1601, a buffer reservoir 1602 with buffer 1604 contained therein, a cap 1603, and a piercing member 1605, as depicted in Fig. 28A. The buffer reservoir 1602 is integral to or detachably fastened to the cap 1603. Moreover, the buffer reservoir 1602 is in a first position relative to the collection vessel 1601 that it is cleared off from the piercing member 1605.

Before use, the cap 1603, together with the buffer reservoir as well as buffer 1602, is removed from the collection vessel 1601, as depicted in Fig. 28B. Subsequently, the piercing member 1605 is also removed from the collection vessel 1601 (Fig. 28C) . A liquid sample 1609 is then put into the collection vessel 1601 (Fig. 28D) .

Subsequently, the piercing member 1605 (Fig. 28E) and the cap 1603, together with the buffer reservoir 1602 as well as buffer 1604 (Fig. 28F) are put back to the collection vessel 1601 such that the buffer reservoir 1602 remains in the first position relative to the collection vessel 1601.

Finally, the cap 1603 is further pressed downward against the collection vessel 1601, which brings the buffer reservoir 1602 to a second position relative to the collection vessel 1602 where the bottom of the buffer reservoir 1602 is pressed against the piercing member 1605. The piercing member 1605 has a plurality of hollow needles deposited thereon which pierce through the bottom of the buffer reservoir 1602, allowing buffer 1604 to flow into the collection vessel and mix with the liquid sample 1609, as depicted in Fig. 28G.

The sample collection unit, together with the collected liquid sample 1609, may be used in the system and/or method of the present disclosure. In some cases, the sample collection unit may be subjected to the sample processing and analysis procedure as described in Example 1.

Example 4: Sample collection unit for swab samples

Figs. 29A-G depict a sample collection unit for swab that can be used for the system and/or method of the present disclosure.

The sample collection unit for swab comprises a collection vessel 1801, a buffer reservoir 1802 with buffer 1804 contained therein, a cap 1803, and a piercing/securing member 1805, as depicted in Fig. 29A. The buffer reservoir 1802 is integral to or detachably fastened to the cap 1803. Moreover, the buffer reservoir 1802 is in a first position relative to the collection vessel 1801 that it is cleared off from the piercing/securing member 1805.

The piercing/securing member 1805 can be detachably fit into the collection vessel via snap fits as depicted in Fig. 29B. The swab sample can be collected on a swab as depicted in Fig. 29C, which comprises a swab head 1810 and a swab stem 1811. The swab head 1810 and the swab stem 1811 can be separated by pulling the swab stem 1811 from the swab head 1810 when the latter is secured.

Before use, the cap 1803, together with the buffer reservoir as well as buffer 1802, is removed from the collection vessel 1801, as depicted in Fig. 29D. The swab is then inserted into the collection vessel 1801 with deposited piercing/securing member 1805 with the swab head contained in the collection vessel 1801 and the swab stem 1811 extending through the opening of the collection vessel 1801, as depicted in Fig. 29E. Both the piercing/securing member 1805 and the swab stem 1811 comprise flaps such that the swab can only be inserted through the piercing/securing member 1805 at certain angles. After the swab is inserted through the piercing/securing member 1805 into the collection vessel 1801, the swab is rotated relative to the piercing/securing member 1805 to allow the flaps on both the piercing/securing member 1805 and the swab stem 1811 to align, as depicted in Fig. 29F. The alignment of flaps allow the swab stem 1811 to be pulled out of the collection vessel 1811 while the swab head 1810 is forced to remain in the collection vessel via obstruction by the flaps on the piercing/securing member 1805, as depicted in Fig. 29G.

Subsequently, the cap 1803, together with the buffer reservoir 1802 as well as buffer 1804 (Fig. 29H) is put back to the collection vessel 1801 such that the buffer reservoir 1802 remains in the first position relative to the collection vessel 1801.

Finally, the cap 1803 is further pressed downward against the collection vessel 1801, which brings the buffer reservoir 1802 to a second position relative to the collection vessel 1802 where the bottom of the buffer reservoir 1802 is pressed against the piercing/securing member 1805. The piercing/securing member 1805 then pierces through the bottom of the buffer reservoir 1802, allowing buffer 1804 to flow into the collection vessel and mix with the swab head 1810, as depicted in Fig. 29H.

The sample collection unit, together with the collected swab head 1810, may be used in the system and/or method of the present disclosure. In some cases, the sample collection unit may be subjected to the sample processing and analysis procedure as described in Example 1.

While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

A system for collecting and/or processing a biological sample of a subject, comprising:

a communication interface in communication with an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in said biological sample of said subject； and

a dispensing unit comprising one or more computer processors operatively coupled to said communication interface, wherein said one or more computer processors are individually or collectively programmed to (a) receive said selection inputted by said user in said display of said electronic device, and (b) direct dispensing of (i) a sample collection unit for collecting said biological sample of said subject, and/or (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection.
The system of claim 1, wherein said one or more graphical elements include a plurality of graphical elements, each of which plurality of graphical elements corresponds to a given target assay among said plurality of target assays.
The system of claim 1, further comprising a sample processing unit that (1) receives said biological sample collected of said subject, and (2) processes said biological sample based on said at least one target assay to determine said presence, absence or amount of said at least one target analyte in said biological sample of said subject.
The system of claim 3, wherein said sample collection unit and/or one or more reagents are included in a kit.
The system of claim 3, wherein said kit includes a finger prick.
The system of claim 3, wherein said kit includes a swap.
The system of claim 3, wherein said dispensing unit includes a plurality of kits including said kit, each of which plurality of kits is directed to a given target assay among said plurality of target assays.
The system of claim 3, wherein said kit is among a plurality of kits, and wherein said one or more computer processors are individually or collectively programmed to (1) monitor a quantity of said plurality of kits or a subset thereof, and (2) provide a notification when said quantity approaches or is below a threshold.
The system of claim 8, wherein said notification is directed over a network to a computer server that receives said notification.
The system of claim 3, wherein said dispensing unit includes an opening to permit dispensing of said kit based on said selection.
The system of claim 3, wherein said kit further comprises instructions for collecting said biological sample from said subject.
The system of claim 1, wherein said at least one target assay includes array hybridization, nucleic acid sequencing or nucleic acid amplification.
The system of claim 1, wherein said dispensing unit is directly coupled to said electronic device.
The system of claim 1, wherein said dispensing unit is remotely coupled to said electronic device.
The system of claim 14, wherein said dispensing unit is operatively coupled to said electronic device over a network.
The system of claim 1, wherein said user interface displays instructions for collecting said biological sample from said subject.
The system of claim 1, wherein said sample collection unit includes identifying information of said subject.
The system of claim 17, wherein said identifying information is anonymous.
The system of claim 17, wherein said identifying information is on a barcode.
The system of claim 17, wherein said identifying information is in a radio-frequency identification (RFID) tag.
The system of claim 1, wherein said user is said subject.
The system of claim 1, wherein said user is a healthcare provider of said subject.
The system of claim 1, wherein said one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for said at least one target analyte.
The system of claim 23, wherein said one or more reagents include a reverse transcriptase and a deoxyribonucleic acid (DNA) polymerase.
The system of claim 1, wherein said one or more reagents include reagents necessary for preserving said biological sample.
The system of claim 1, wherein said biological sample includes a soil or food sample.
The system of claim 26, wherein said food sample is a dairy sample.
The system of claim 26, wherein said dairy sample includes milk.
The system of claim 1, wherein said biological sample is a tissue or fluid of a subject.
The system of claim 29, wherein said tissue or fluid is stool.
The system of claim 29, wherein said biological sample is an oral or rectal swab.
The system of claim 1, wherein said one or more graphical elements permit said user to input a selection of one or more of a tissue type of said biological sample and disease.
The system of claim 32, wherein said disease is selected from a plurality of diseases.
The system of claim 32, wherein said disease is cancer.
The system of claim 1, wherein said at least one target analyte is associated with a disease.
The system of claim 35, wherein said disease is associated with a virus.
The system of claim 36, wherein said virus is an RNA virus.
The system of claim 36, wherein said virus is a DNA virus.
The system of claim 36, wherein said virus is selected from the group consisting of human immunodeficiency virus I (HIV I) , human immunodeficiency virus II (HIV II) , an orthomyxovirus, Ebola virus, Dengue virus, influenza viruses, hepevirus, hepatitis A virus, hepatitis B virus, hepatitis C virus, hepatitis D virus, hepatitis E virus, hepatitis G virus, Epstein-Barr virus, mononucleosis virus, cytomegalovirus, SARS virus, West Nile Fever virus, polio virus, measles virus, herpes simplex virus, smallpox virus, adenovirus, Coxsackie virus, and Varicella virus.
The system of claim 39, wherein said influenza virus is selected from the group consisting of H1N1 virus, H3N2 virus, H7N9 virus and H5N1 virus.
The system of claim 39, wherein said adenovirus is adenovirus type 55 (ADV55) or adenovirus type 7 (ADV7) .
The system of claim 39, wherein said hepatitis C virus is armored RNA-hepatitis C virus (RNA-HCV) .
The system of claim 39, wherein said Coxsackie virus is Coxsackie virus A16.
The system of claim 35, wherein said disease is associated with a pathogenic bacterium or a pathogenic protozoan.
The system of claim 44, wherein said pathogenic bacterium is a gram-positive or gram-negative pathogenic bacterium.
The system of claim 44, wherein said pathogenic bacterium is selected from the group consisting of Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Enterobacter sakazakii, Vibrio Parahemolyticus, and Shigella spp.
The system of claim 44, wherein said pathogenic bacterium is Mycobacterium tuberculosis.
The system of claim 44, wherein said pathogenic protozoan is Plasmodium.
The system of claim 44, wherein said pathogenic bacterium is Salmonella.
The system of claim 1, wherein said at least one target assay is an amplification protocol.
The system of claim 1, wherein said plurality of target assays are directed to different target analytes.
The system of claim 1, wherein said plurality of target assays are the same type of assay.
The system of claim 1, wherein said amount is a relative amount.
The system of claim 1, wherein said system has a footprint less than or equal to 100 feet².
The system of claim 54, wherein said footprint is less than or equal to 25 feet².
The system of claim 54, wherein said footprint is less than or equal to 9 feet².
The system of claim 1, wherein said dispensing unit has a footprint less than or equal to 100 feet².
The system of claim 57, wherein said footprint is less than or equal to 25 feet².
The system of claim 57, wherein said footprint is less than or equal to 9 feet².
The system of claim 1, wherein said dispensing unit is within 5 feet of said electronic device.
The system of claim 60, wherein said dispensing unit is within 1 foot of said electronic device.
The system of claim 1, wherein said dispensing unit is attached to said electronic device.
The system of claim 1, wherein said sample collection unit is selected based on a type of said biological sample.
The system of claim 1, wherein said electronic device is a mobile electronic device of said user or said subject.
The system of claim 1, wherein said dispensing unit is operatively coupled to said electronic device through said communication interface.
The system of claim 1, wherein said communication interface is in communication with said electronic device over a network.
The system of claim 1, wherein said communication interface is in communication with said electronic device through at least one electronic bus.
The system of claim 1, wherein said electronic device further includes a sensing unit that captures a characteristic of said subject.
The system of claim 68, wherein said one or more computer processors are individually or collectively programmed to receive said selection inputted by said user subsequent to said user being provided said characteristic.
The system of claim 68, wherein said characteristic is a sound, image or video having said subject.
The system of claim 68, wherein said characteristic is a temperature, resistance, impedance, capacitance of said subject.
The system of claim 1, wherein said communication interface is in communication with an authentication unit that authenticates said user.
The system of claim 72, wherein said authentication unit is a fingerprint scanner, retina scanner, or impedance scanner.
The system of claim 73, wherein said authentication unit is part of said electronic device.
The system of claim 74, wherein said authentication unit is part of said system.
An electronic device for processing a biological sample of a subject, comprising:

a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in a biological sample of a subject； and

one or more computer processors operatively coupled to said display screen, wherein said one or more computer processors are individually or collectively programmed to (a) receive said selection inputted by said user in said user interface, and (b) transmit said selection to a dispensing unit that directs dispensing of (i) a sample collection unit for collecting said biological sample of said subject, and/or (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection.
The electronic device of claim 76, wherein said one or more graphical elements are part of a questionnaire displayed on said user interface, which questionnaire (i) provides one or more questions to said user and (ii) generates an output based on one or more responses of said user to said one or more questions, which output corresponds to said at least one target assay from said plurality of target assays
The electronic device of claim 77, wherein said questionnaire is a guided questionnaire.
The electronic device of claim 76, wherein said user is said subject.
The electronic device of claim 76, wherein said user is a healthcare provider of said subject.
The electronic device of claim 76, wherein said electronic device is a mobile electronic device of said user or said subject.
The electronic device of claim 76, wherein said display screen is a capacitive touch screen or resistive touch screen.
The electronic device of claim 76, further comprising a communication interface that brings said one or more computer processors in communication with said dispensing unit.
The electronic device of claim 76, further comprising a sensing unit that captures a characteristic of said subject.
The electronic device of claim 84, wherein said one or more computer processors are individually or collectively programmed to receive said selection inputted by said user subsequent to said user being provided said characteristic of said subject.
The electronic device of claim 84, wherein said characteristic is a sound, image or video having said subject.
The electronic device of claim 84, wherein said characteristic is a temperature, resistance, impedance, capacitance of said subject.
The electronic device of claim 76, wherein said one or more computer processors are in communication with an authentication unit that authenticates said user.
The electronic device of claim 88, wherein said authentication unit is a fingerprint scanner, retina scanner, or impedance scanner.
The electronic device of claim 88, wherein said authentication unit is part of said electronic device.
A system for processing a biological sample of a subject, comprising:

a communication interface in communication with (i) an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining a presence, absence or amount of at least one target analyte in said biological sample of said subject, and (ii) a dispensing unit that dispenses a kit based on said selection, wherein said kit comprises (1) a sample collection unit for collecting said biological sample of said subject, and (2) one or more reagents necessary for processing said biological sample of said subject based on said selection； and

a sample processing unit operatively coupled to said communication interface, wherein said sample processing unit (a) receives said biological sample of said subject, and (b) processes said biological sample based on said selection inputted by said user corresponding to said at least one target assay from said plurality of target assays, to determine said presence, absence or amount of said at least one target analyte in said biological sample of said subject.
The system of claim 91, wherein said sample processing unit comprises an actuator that transfers said biological sample to or from one or more sample processing stations of said sample processing unit.
The system of claim 92, wherein said actuator is a robotic arm.
The system of claim 91, wherein said one or more graphical elements include a plurality of graphical elements, each of which plurality of graphical elements corresponds to a given target assay among said plurality of target assays.
The system of claim 91, wherein said at least one target assay is an amplification protocol.
The system of claim 91, wherein said sample processing unit receives said biological sample in a sample collection unit.
The system of claim 96, wherein said sample collection unit includes a cap.
The system of claim 96, wherein said sample collection unit includes identifying information of said subject.
The system of claim 98, wherein said identifying information is anonymous.
The system of claim 98, wherein said identifying information is on a barcode.
The system of claim 98, wherein said identifying information is in a radio-frequency identification (RFID) tag.
The system of claim 91, wherein said at least one target assay includes array hybridization, nucleic acid sequencing or nucleic acid amplification.
The system of claim 91, wherein said sample processing unit is directly coupled to said electronic device.
The system of claim 91, wherein said sample processing unit is remotely coupled to said electronic device.
The system of claim 104, wherein said sample processing unit is operatively coupled to said electronic device over a network.
The system of claim 91, wherein said electronic device is a mobile electronic device of said user or said subject.
The system of claim 91, wherein said sample processing unit includes an opening to permit said user to deposit said biological sample.
The system of claim 91, wherein said user is said subject.
The system of claim 91, wherein said one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for said at least one target analyte,
The system of claim 109, wherein said one or more reagents include a reverse transcriptase and a deoxyribonucleic acid (DNA) polymerase.
The system of claim 91, wherein said one or more reagents include reagents necessary for preserving said biological sample.
The system of claim 91, wherein said biological sample includes a soil or food sample.
The system of claim 112, wherein said food sample is a dairy sample.
The system of claim 112, wherein said dairy sample includes milk.
The system of claim 91, wherein said biological sample is a tissue or fluid of a subject
The system of claim 115, wherein said tissue or fluid is stool.
The system of claim 115, wherein said biological sample is an oral or rectal swab.
The system of claim 91, wherein said one or more graphical elements permit said user to input a selection of one or more of a tissue type of said biological sample and disease.
The system of claim 118, wherein said disease is selected from a plurality of diseases
The system of claim 118, wherein said disease is cancer
The system of claim 91, wherein said at least one target analyte is associated with a disease.
The system of claim 121, wherein said disease is associated with a virus.
The system of claim 122, wherein said virus is an RNA virus.
The system of claim 122, wherein said virus is a DNA virus.
The system of claim 122, wherein said virus is selected from the group consisting of human immunodeficiency virus I (HIV I) , human immunodeficiency virus II (HIV II) , an orthomyxovirus, Ebola virus, Dengue virus, influenza viruses, hepevirus, hepatitis A virus, hepatitis B virus, hepatitis C virus, hepatitis D virus, hepatitis E virus, hepatitis G virus, Epstein-Barr virus, mononucleosis virus, cytomegalovirus, SARS virus, West Nile Fever virus, polio virus, measles virus, herpes simplex virus, smallpox virus, adenovirus, Coxsackie virus, and Varicella virus.
The system of claim 125, wherein said influenza virus is selected from the group consisting of H1N1 virus, H3N2 virus, H7N9 virus and H5N1 virus.
The system of claim 125, wherein said adenovirus is adenovirus type 55 (ADV55) or adenovirus type 7 (ADV7) .
The system of claim 125, wherein said hepatitis C virus is armored RNA-hepatitis C virus (RNA-HCV) .
The system of claim 125, wherein said Coxsackie virus is Coxsackie virus A16.
The system of claim 121, wherein said disease is associated with a pathogenic bacterium or a pathogenic protozoan.
The system of claim 130, wherein said pathogenic bacterium is a gram-positive or gram-negative pathogenic bacterium.
The system of claim 130, wherein said pathogenic bacterium is selected from the group consisting of Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Enterobacter sakazakii, Vibrio Parahemolyticus, and Shigella spp.
The system of claim 130, wherein said pathogenic bacterium is Mycobacterium tuberculosis.
The system of claim 130, wherein said pathogenic protozoan is Plasmodium.
The system of claim 130, wherein said pathogenic bacterium is Salmonella.
The system of claim 91, wherein said plurality of target assays are directed to different target analytes.
The system of claim 91, wherein said plurality of target assays are the same type of assay.
The system of claim 91, wherein said amount is a relative amount.
The system of claim 91, wherein said system has a footprint less than or equal to 100 feet².
The system of claim 139, wherein said footprint is less than or equal to 25 feet².
The system of claim 139, wherein said footprint is less than or equal to 9 feet².
The system of claim 91, wherein said sample processing unit has a footprint less than or equal to 100 feet².
The system of claim 142, wherein said footprint is less than or equal to 25 feet².
The system of claim 142, wherein said footprint is less than or equal to 9 feet².
The system of claim 91, wherein said sample processing unit is within 5 feet of said electronic device.
The system of claim 145, wherein said sample processing unit is within 1 foot of said electronic device.
The system of claim 91, wherein said sample processing unit is attached to said electronic device.
The system of claim 91, wherein said sample processing unit authenticates said subject.
The system of claim 91, wherein said sample processing unit is operatively coupled to said electronic device through said communication interface.
The system of claim 91, wherein said sample processing unit is operatively coupled to said electronic device through said communication interface.
The system of claim 91, wherein said communication interface is in communication with said electronic device over a network.
The system of claim 91, wherein said communication interface is in communication with said electronic device through at least one electronic bus.
The system of claim 91, wherein said electronic device further includes a sensing unit that captures a characteristic of said subject.
The system of claim 153, wherein said one or more computer processors are individually or collectively programmed to receive said selection inputted by said user subsequent to said user being provided said characteristic.
The system of claim 153, wherein said characteristic is a sound, image or video having said subject.
The system of claim 153, wherein said characteristic is a temperature, resistance, impedance, capacitance of said subject.
The system of claim 91, wherein said communication interface is in communication with an authentication unit that authenticates said user.
The system of claim 157, wherein said authentication unit is a fingerprint scanner, retina scanner, or impedance scanner.
The system of claim 157, wherein said authentication unit is part of said electronic device.
The system of claim 157, wherein said authentication unit is part of said system.
A system for collecting and/or processing a biological sample of a subject, comprising:

a dispensing unit that autonomously dispenses a kit based on a selection provided by a user corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining a presence, absence or amount of at least one target analyte in said biological sample of said subject, wherein said kit comprises (i) a sample collection unit for collecting said biological sample of said subject, and/or (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection； and

a sample processing unit operatively coupled to said dispensing unit, wherein said sample processing unit (a) receives said biological sample collected from said subject using said kit, and (b) processes said biological sample based on said selection inputted by said user corresponding to said at least one target assay from said plurality of target assays, to determine said presence, absence or amount of said at least one target analyte in said biological sample of said subject.
The system of claim 161, wherein said dispensing unit and said sample processing unit are in a housing.
The system of claim 162, wherein said housing has a footprint less than or equal to 100 feet².
The system of claim 163, wherein said footprint is less than or equal to 25 feet².
The system of claim 163, wherein said footprint is less than or equal to 9 feet².
The system of claim 161, wherein said kit comprises (i) a sample collection unit for collecting said biological sample of said subject, and (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection.
The system of claim 161, wherein said sample processing unit comprises an actuator that transfers said biological sample to or from one or more sample processing stations of said sample processing unit.
The system of claim 167, wherein said actuator is a robotic arm.
The system of claim 161, further comprising an electronic device operatively coupled to said dispensing unit, wherein said electronic device provides said selection to said dispensing unit.
The system of claim 161, wherein said kit includes a finger prick.
The system of claim 161, wherein said kit includes a swap.
The system of claim 161, wherein said at least one target assay includes array hybridization, nucleic acid sequencing or nucleic acid amplification.
The system of claim 161, wherein said dispensing unit includes an opening to permit dispensing of said kit based on said selection.
The system of claim 161, wherein said sample collection unit includes identifying information of said subject.
The system of claim 174, wherein said identifying information is anonymous.
The system of claim 174, wherein said identifying information is on a barcode.
The system of claim 174, wherein said identifying information is in a radio-frequency identification (RFID) tag.
The system of claim 161, wherein said user is said subject.
The system of claim 161, wherein said one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for said at least one target analyte.
The system of claim 179, wherein said one or more reagents include a reverse transcriptase and a deoxyribonucleic acid (DNA) polymerase.
The system of claim 161, wherein said one or more reagents include reagents necessary for preserving said biological sample.
The system of claim 161, wherein said sample processing unit receives said biological sample in said sample collection unit.
The system of claim 182, wherein said sample collection unit includes a cap
The system of claim 182, wherein said sample collection unit includes identifying information of said subject.
The system of claim 184, wherein said identifying information is anonymous.
The system of claim 184, wherein said identifying information is on a barcode.
The system of claim 184, wherein said identifying information is in a radio-frequency identification (RFID) tag.
The system of claim 161, wherein said plurality of target assays are directed to different target analytes.
The system of claim 161, wherein said plurality of target assays are the same type of assay.
The system of claim 161, wherein said at least one target assay is an amplification protocol.
The system of claim 161, wherein said amount is a relative amount.
The system of claim 161, wherein said system has a footprint less than or equal to 100 feet².
The system of claim 192, wherein said footprint is less than or equal to 25 feet².
The system of claim 192, wherein said footprint is less than or equal to 9 feet².
The system of claim 161, wherein said sample processing unit is within 5 feet of said dispensing unit
The system of claim 195, wherein said sample processing unit is within 1 foot of said dispensing unit.
The system of claim 161, wherein said sample processing unit is attached to said dispensing unit
The system of claim 161, wherein said sample collection unit is selected based on a type of said biological sample
A system for collecting a biological sample of a subject, comprising:

one or more computer processors that are individually or collectively programmed to (i) authenticate said subject from which said biological sample is to be collected, and (ii) receive a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in said biological sample of said subject； and

a dispensing unit operatively coupled to said one or more computer processors, wherein said dispensing unit, upon authentication of said subject, autonomously directs dispensing of (i) a sample collection unit for collecting said biological sample of said subject, and/or (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection.
The method of claim 199, further comprising an authentication unit operatively coupled to said one or more computer processors, wherein said authentication unit authenticates said user.
The method of claim 200, wherein said authentication unit is a fingerprint scanner, retina scanner, or impedance scanner.
The method of claim 199, wherein said sample collection unit and/or one or more reagents are included in a kit.
The method of claim 202, wherein said kit includes a finger prick.
The method of claim 202, wherein said kit includes a swap.
The method of claim 202, wherein said kit further comprises instructions for collecting said biological sample from said subject.
The method of claim 199, further comprising a sample processing unit that (1) receives said biological sample collected of said subject, and (2) processes said biological sample based on said at least one target assay to determine said presence, absence or amount of said at least one target analyte in said biological sample of said subject.
The method of claim 199, wherein said sample collection unit includes identifying information of said subject.
The method of claim 207, wherein said identifying information is anonymous.
The method of claim 207, wherein said identifying information is on a barcode.
The method of claim 207, wherein said identifying information is in a radio-frequency identification (RFID) tag.
The method of claim 199, wherein said user is said subject.
The method of claim 199, wherein said user is a healthcare provider of said subject
A method for collecting a biological sample of a subject, comprising:

(a) establishing communication between a dispensing unit and an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in said biological sample of said subject；

(b) receiving said selection inputted by said user in said display of said electronic device； and

(c) using said dispensing unit to direct dispensing of (i) a sample collection unit for collecting said biological sample of said subject, and/or (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection.
The method of claim 213, further comprising receiving said biological sample collected from said subject at a sample processing unit that processes said biological sample based on said at least one target assay to determine said presence, absence or amount of said at least one target analyte in said biological sample of said subject.
The method of claim 213, wherein said one or more graphical elements include a plurality of graphical elements, each of which plurality of graphical elements corresponds to a given target assay among said plurality of target assays.
The method of claim 213, wherein said kit includes a finger prick.
The method of claim 213, wherein said kit includes a swap.
The method of claim 213, wherein said at least one target assay includes array hybridization, nucleic acid sequencing or nucleic acid amplification.
The method of claim 213, wherein said electronic device is a mobile electronic device of said user or said subject.
The method of claim 213, wherein said kit is among a plurality of kits.
The method of claim 220, further comprising monitoring a quantity of said plurality of kits or a subset thereof, and providing a notification when said quantity approaches or is below a threshold.
The method of claim 221, wherein said notification is directed over a network to a computer server that receives said notification.
The method of claim 213, wherein said sample collection unit includes identifying information of said subject.
The method of claim 223, wherein said identifying information is anonymous.
The method of claim 223, wherein said identifying information is on a barcode.
The method of claim 223, wherein said identifying information is in a radio-frequency identification (RFID) tag.
The method of claim 213, wherein said user is said subject.
The method of claim 213, wherein said one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for said at least one target analyte.
The method of claim 228, wherein said one or more reagents include a reverse transcriptase and a deoxyribonucleic acid (DNA) polymerase.
The method of claim 213, wherein said one or more reagents include reagents necessary for preserving said biological sample.
The method of claim 213, wherein said biological sample includes a soil or food sample.
The method of claim 213, wherein said biological sample is a tissue or fluid of a subject.
The method of claim 213, wherein said one or more graphical elements permit said user to input a selection of one or more of a tissue type of said biological sample and disease.
The method of claim 213, wherein said at least one target analyte is associated with a disease.
The method of claim 213, wherein said at least one target assay is an amplification protocol.
The method of claim 213, wherein said plurality of target assays are directed to different target analytes.
The method of claim 213, wherein said plurality of target assays are the same type of assay.
The method of claim 213, wherein said amount is a relative amount.
A method for processing a biological sample of a subject, comprising:

(a) activating a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in a biological sample of a subject；

(b) receiving said selection inputted by said user in said user interface； and

(c) transmitting said selection to a dispensing unit that directs dispensing of (i) a sample collection unit for collecting said biological sample of said subject, and/or (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection.
The method of claim 239, wherein said one or more graphical elements are part of a questionnaire displayed on said user interface.
The method of claim 240, further comprising using said questionnaire to (i) provide one or more questions to said user and (ii) generate an output based on one or more responses of said user to said one or more questions, which output corresponds to said at least one target assay from said plurality of target assays.
The method of claim 240, wherein said questionnaire is a guided questionnaire.
The method of claim 239, further comprising capturing a characteristic of said subject using a sensing unit and providing said characteristic to said user.
The method of claim 243, further comprising receiving said selection inputted by said user subsequent to said user being provided said characteristic of said subject.
The method of claim 243, wherein said characteristic is a sound, image or video having said subject.
The method of claim 243, wherein said characteristic is a temperature, resistance, impedance, capacitance of said subject.
A method for processing a biological sample of a subject, comprising:

(a) establishing communication between a sample processing unit and an electronic device that comprises a display screen having a user interface that displays one or more graphical elements that permit a user to input a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining a presence, absence or amount of at least one target analyte in said biological sample of said subject；

(b) receiving said biological sample from said subject at said sample processing unit； and

(c) using said sample processing unit to process said biological sample based on said selection inputted by said user corresponding to said at least one target assay from said plurality of target assays, to determine said presence, absence or amount of said at least one target analyte in said biological sample of said subject.
The method of claim 247, further comprising using a dispensing unit to dispense a kit based on said selection, wherein said kit comprises (i) a sample collection unit for collecting said biological sample of said subject, and (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection.
The method of claim 247, wherein said at least one target assay is an amplification protocol.
The method of claim 247, wherein said sample processing unit receives said biological sample in a sample collection unit.
The method of claim 250, wherein said sample collection unit includes a cap.
The method of claim 250, wherein said sample collection unit includes identifying information of said subject.
The method of claim 252, wherein said identifying information is anonymous.
The method of claim 252, wherein said identifying information is on a barcode.
The method of claim 252, wherein said identifying information is in a radio-frequency identification (RFID) tag.
The method of claim 247, wherein said at least one target assay includes array hybridization, nucleic acid sequencing or nucleic acid amplification.
The method of claim 247, wherein said one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for said at least one target analyte.
The method of claim 257, wherein said one or more reagents include a reverse transcriptase and a deoxyribonucleic acid (DNA) polymerase.
The method of claim 247, wherein said one or more reagents include reagents necessary for preserving said biological sample.
The method of claim 247, wherein said biological sample includes a soil or food sample.
The method of claim 247, wherein said biological sample is a tissue or fluid of a subject.
The method of claim 247, wherein said one or more graphical elements permit said user to input a selection of one or more of a tissue type of said biological sample and disease.
The method of claim 247, wherein said at least one target analyte is associated with a disease.
The method of claim 247, wherein said plurality of target assays are directed to different target analytes.
The method of claim 247, wherein said plurality of target assays are the same type of assay.
The method of claim 247, wherein said amount is a relative amount.
A method for collecting and/or processing a biological sample of a subject, comprising:

(a) using a dispensing unit to dispense a kit based on a selection provided by a user corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining a presence, absence or amount of at least one target analyte in said biological sample of said subject, wherein said kit comprises (i) a sample collection unit for collecting said biological sample of said subject, and/or (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection； and

(b) receiving said biological sample collected from said subject using said kit at a sample processing unit operatively coupled to said dispensing unit； and

(c) using said sample processing unit to process said biological sample based on said selection inputted by said user corresponding to said at least one target assay from said plurality of target assays, to determine said presence, absence or amount of said at least one target analyte in said biological sample of said subject.
The method of claim 267, further comprising directing said selection from an electronic device to said dispensing unit.
The method of claim 267, wherein said kit includes a finger prick.
The method of claim 267, wherein said kit includes a swap.
The method of claim 267, wherein said at least one target assay includes array hybridization, nucleic acid sequencing or nucleic acid amplification.
The method of claim 267, wherein said user is said subject.
The method of claim 267, wherein said one or more reagents are selected from the group consisting of a reverse transcriptase, a polymerizing enzyme and a primer set for said at least one target analyte,
The method of claim 273, wherein said one or more reagents include a reverse transcriptase and a deoxyribonucleic acid (DNA) polymerase.
The method of claim 267, wherein said one or more reagents include reagents necessary for preserving said biological sample.
The method of claim 267, wherein said sample processing unit receives said biological sample in said sample collection unit.
The method of claim 267, wherein said plurality of target assays are directed to different target analytes.
The method of claim 267, wherein said plurality of target assays are the same type of assay.
The method of claim 267, wherein said at least one target assay is an amplification protocol.
The method of claim 267, wherein said amount is a relative amount.
A method for collecting a biological sample of a subject, comprising:

(a) authenticating said subject from which said biological sample is to be collected；

(b) receiving a selection corresponding to at least one target assay from a plurality of target assays, which at least one target assay is directed to determining presence, absence or amount of at least one target analyte in said biological sample of said subject； and

(c) upon authenticating said subject, using a dispensing unit to autonomously direct dispensing of (i) a sample collection unit for collecting said biological sample of said subject, and/or (ii) one or more reagents necessary for processing said biological sample of said subject based on said selection.
The method of claim 281, wherein said at least one target assay is an amplification protocol.
The method of claim 281, wherein said biological sample includes a soil or food sample.
The method of claim 283, wherein said food sample is a dairy sample.
The method of claim 284, wherein said dairy sample includes milk.
The method of claim 281, wherein said biological sample is a tissue or fluid of a subject.
The method of claim 286, wherein said tissue or fluid is stool.
The method of claim 286, wherein said biological sample is an oral or rectal swab.
The method of claim 281, wherein said sample collection unit includes a cap.
The method of claim 281, wherein said sample collection unit includes identifying information of said subject.