HK40048936B - Flow cells and methods related to same - Google Patents

Description

Flow cells and related methods

Cross-reference to related applications

This patent application claims priority to U.S. Provisional Patent Application No. 62/731,785, filed September 14, 2018, entitled Flow Cell and Methods Therewith. The entire contents of the above application are incorporated herein by reference.

Background Technology

Various protocols in biological or chemical research are designed to conduct numerous controlled experiments on a locally supported surface or within a predefined reaction chamber. Specific reactions can then be observed or detected, and subsequent analysis can help identify or reveal the properties of the substances involved in the reaction. For example, in some multiplex identification schemes, an unknown analyte with an identifiable label (e.g., a fluorescent label) can be exposed to thousands of known probes under controlled conditions. Each known probe can be placed into a corresponding well in a microplate. Observing any chemical reactions occurring between the known probe and the unknown analyte in the well can help identify or reveal the properties of the analyte. Other examples of such protocols include known DNA sequencing procedures, such as sequencing by synthesis (SBS) or circular array sequencing.

In some traditional fluorescence detection procedures, optical systems are used to direct excitation light onto a fluorescently labeled analyte and detect any fluorescence signals that may be emitted from the analyte. However, such optical systems can be relatively expensive and involve a relatively large stage footprint. For example, such optical systems may include the arrangement of lenses, filters, and light sources.

In other proposed detection systems, the controlled reaction occurs within a predefined reaction chamber on a localized support surface or in a flow cell that does not involve a large optical component support for detecting fluorescence emission. The flow cell contains an electronic solid-state photodetector or imager (e.g., a complementary metal-oxide-semiconductor (CMOS) photodetector or charge-coupled device (CCD) photodetector) positioned near (e.g., below) the support surface/reaction chamber to detect the light emission generated by the reaction. However, such proposed solid-state imaging systems may have some limitations. For example, the flow cell in such systems may be designed as a single-use consumable. Therefore, it may be advantageous for the flow cell to be a small and inexpensive device. In a relatively small flow cell, it may be beneficial to utilize as much of the biosensor's effective area as possible and/or provide the largest possible effective area for the biodetector.

Many existing flow cell designs do not allow for full utilization of the effective region of a biodetector because the flow cell cap portion is connected to the effective region, preventing reagent solutions (e.g., solutions of fluorescently labeled molecules) from reaching such regions and/or preventing these regions from containing reaction sites (e.g., containing analytes). Furthermore, the effective region of a biodetector is typically provided by a single sensor, and relatively large sensors with relatively large effective regions are expensive. Many existing flow cell designs also offer only a limited number of wiring configurations for optical detection devices.

Summary of the Invention

In one aspect of the invention, a flow cell is provided. The flow cell includes a support frame comprising a top side, a back side, and at least one cavity extending from the top side to a bottom side. The flow cell further includes at least one photodetector disposed within the at least one cavity, the at least one cavity including an effective region and an upper surface. The flow cell also includes a support material disposed within the at least one cavity between the support frame and the periphery of the at least one photodetector, coupling the support frame and the at least one photodetector together. The flow cell further includes a cap extending above the at least one photodetector and coupled to the top side of the support frame around the periphery of the at least one photodetector. The cap and at least the upper surface of the at least one photodetector form a fluid channel therebetween.

In some examples, the support frame further includes at least one conductive via extending from the top side to the bottom side. In some such examples, at least one photodetector includes at least one solid-state photodetector comprising a base wafer portion, a plurality of photosensors, device circuitry electrically coupled to the photosensors to transmit photon data signals detected by the photosensors, and a plurality of light guides associated with the plurality of photosensors. In some such examples, the device circuitry of the at least one solid-state photodetector is electrically coupled to at least one conductive via on the top side of the support frame.

In some examples, the cover is indirectly coupled to the top side of the support frame. In some examples, at least one cavity includes a cavity in which multiple light detection devices are disposed. In some such examples, the multiple light detection devices include different light detection devices spaced apart from each other, and the support material further extends between adjacent light detection devices. In some other such examples, the multiple light detection devices include at least two integrated light detection devices, and the support material extends between the support frame and the outer periphery of the at least two integrated light detection devices.

In some examples, at least one photodetector includes multiple photodetectors. In some such examples, at least one cavity includes multiple cavities, each of the multiple photodetectors being disposed in a different cavity within the support frame. In some examples, at least one photodetector includes at least one solid-state photodetector comprising a base wafer portion, multiple photosensors, device circuitry electrically coupled to the photosensors to transmit photon data signals detected by the photosensors, and multiple light guides associated with the multiple photosensors. In some such examples, at least one cavity extends through the support frame from top to bottom, the device circuitry including vias extending through the base wafer portion, and the flow cell further including electrical contacts disposed at least partially along the back side of the support frame and electrically coupled to the vias. In some other such examples, the at least one photodetector further includes a reaction structure disposed above the multiple light guides forming their upper surfaces, the reaction structure including multiple nanopores positioned within an effective region.

In some examples, at least one cavity extends only partially through the support frame from the top to the bottom side. In some examples, at least one light detection device includes at least one complementary metal-oxide-semiconductor (CMOS) light sensor.

In some examples, the fluid channel extends over the entire effective area of at least one optical detection device.

In another aspect of the invention, a method is provided. The method includes attaching an upper surface of a support frame to a planar support surface of a substrate, the support frame including at least one cavity extending from its top side to its bottom side. The method further includes positioning at least one photodetector within the at least one cavity such that its top side is positioned on the planar support surface of the substrate, and an edge portion of the cavity extends between the support frame and the outer periphery of the at least one photodetector, the at least one photodetector including an effective region and an upper surface. The method also includes filling the edge portion of the cavity with a support material to couple the support frame and the at least one photodetector together. The method further includes separating the support frame and the substrate. The method also includes attaching a cap around the outer periphery of the at least one photodetector to the top side of the support frame to form a flow pool, the cap extending above the at least one photodetector and forming a fluid channel between the cap and at least the upper surface of the at least one photodetector.

In some examples, the at least one optical detection device includes at least one solid-state optical detection device comprising a base wafer portion forming a back side, a plurality of optical sensors, device circuitry electrically coupled to the optical sensors to transmit photon data signals based on the photons detected by the optical sensors, and a plurality of light guides associated with the plurality of optical sensors, and the support frame further includes at least one conductive via extending from the top side to the bottom side, the method further comprising electrically coupling the device circuitry of the at least one solid-state optical detection device to the at least one conductive via on the top side of the support frame.

In some examples, at least one optical detection device includes at least one solid-state optical detection device comprising a base wafer portion forming a back side, a plurality of optical sensors, device circuitry electrically coupled to the optical sensors to transmit photon data signals based on those detected by the optical sensors, and a plurality of light guides associated with the plurality of optical sensors. The device circuitry includes vias extending through the base wafer portion to its back side, and the method further includes electrically coupled contacts arranged at least partially along the back side of the support frame to the vias on the back side of the substrate portion.

In some examples, the method further includes forming a reactive structure on the at least one photodetector device prior to attaching the cap, the reactive structure forming an upper surface of at least one photodetector device and including a plurality of nanopores positioned within an effective region. In some such examples, separating the support frame and the substrate exposes a recessed top side of a support material extending between the top surface of the support frame and the top of the at least one photodetector device, wherein the reactive structure extends on the recessed top side of the support material and the top side of the support frame, and wherein the reactive structure forms a planar top surface from which the plurality of nanopores extend.

In some examples, the method further includes obtaining at least one light detection device, which includes cutting at least one complementary metal-oxide-semiconductor (CMOS) light sensor from a plurality of integrated CMOS light sensors.

In some examples, the fluid channel extends over the entire effective area of at least one optical detection device.

In another aspect of the invention, another method is provided. The method includes disposing a first support material on the bottom portion of at least one cavity of a support frame, said at least one cavity extending only partially from the top side to the bottom side of the support frame. The method further includes positioning at least one photodetector within the at least one cavity and above the disposed first support material, such that an edge portion of said at least one cavity extends between the support frame and the outer periphery of said at least one photodetector, said at least one photodetector including an effective region and a top surface. The method also includes filling the edge portion of the cavity with a second support material. The method further includes attaching a cap to the top side of the support frame around the periphery of said at least one photodetector to form a flow pool, said cap extending above said at least one photodetector and forming a fluid channel between said cap and at least the top surface of said at least one photodetector.

In some examples, the fluid channel extends over the entire effective area of at least one optical detection device.

It should be understood that all combinations of the foregoing aspects and other concepts discussed in more detail below (provided that such concepts do not contradict each other) are considered to be part of the subject matter of the invention and realize the advantages disclosed herein.

These and other objectives, features, and advantages of the invention will become apparent from the following detailed description of various aspects of the invention, taken in conjunction with the accompanying drawings.

Attached Figure Description

These and other features, aspects, and advantages of the invention will be better understood when the following detailed description is read with reference to the accompanying drawings, which are not necessarily drawn to scale. In the drawings, similar reference numerals denote similar aspects, wherein:

Figure 1 illustrates a cross-sectional view of a light detection device according to one or more aspects of the present invention in one example.

Figure 2 illustrates a cross-sectional view of another optical detection device according to one or more aspects of the present invention in one example.

Figure 3 illustrates, in one example, a support structure consisting of a support frame and a substrate for forming a flow pool according to one or more aspects of the present invention.

Figure 4 illustrates, in one example, the positioning of a light detection device within the cavity of the support structure of Figure 3 according to one or more aspects of the invention.

Figure 5 illustrates, in one example, a cross-sectional view of a light detection device positioned within a cavity of the support structure of Figure 3 according to one or more aspects of the present invention.

Figure 6 illustrates, in one example, a cross-sectional view of a light detection device positioned within a cavity of another support structure according to one or more aspects of the present invention.

Figure 7 illustrates, in one example, a cross-sectional view of a light detection device positioned within a cavity of another support structure according to one or more aspects of the present invention.

Figure 8 illustrates, in one example, a cross-sectional view of a light detection device positioned within a cavity of another support structure according to one or more aspects of the present invention.

Figure 9 illustrates, in one example, a cavity extending outward from the periphery of a light detection device located within a cavity of a support structure of Figure 4, filled with material according to one or more aspects of the invention.

Figure 10 illustrates, in one example, the removal of a substrate from the support frame of the support structure of Figure 4 according to one or more aspects of the present invention.

Figure 11A illustrates, in one example, a cross-sectional view of multiple photodetectors coupled within multiple cavities of the support frame of Figure 4 with the substrate removed, according to one or more aspects of the present invention.

Figure 11B illustrates, in one example, a top view of a plurality of optical detection devices coupled within a cavity of a support frame of Figure 11A according to one or more aspects of the invention.

Figure 12A illustrates, in one example, a cross-sectional view of a plurality of photodetectors coupled within a cavity of a support frame with a removed substrate, according to one or more aspects of the present invention.

Figure 12B illustrates, in one example, a top view of a plurality of optical detection devices coupled within a cavity of a support frame of Figure 12A according to one or more aspects of the present invention.

Figure 13A illustrates, in one example, a cross-sectional view of a plurality of photodetectors coupled within another cavity of a support frame with the substrate removed, according to one or more aspects of the invention.

Figure 13B illustrates, in one example, a top view of a plurality of optical detection devices coupled within a cavity of a support frame of Figure 13A according to one or more aspects of the present invention.

Figure 14 illustrates, in one example, a cross-sectional view of multiple optical detection devices coupled within a cavity of another support frame according to one or more aspects of the present invention.

Figure 15A illustrates, in one example, a cross-sectional view of a light detection device according to one or more aspects of the present invention and the filling material within the cavity of a support frame.

Figure 15B illustrates, in one example, a cross-sectional view of the photodetector of Figure 15A in which a reactive structure according to one or more aspects of the present invention is positioned, and the filling material within the cavity of the support frame.

Figure 16A illustrates, in one example, a cross-sectional view of an intermediate flow cell device comprising multiple optical detection devices coupled within multiple cavities of a support frame, according to one or more aspects of the present invention.

Figures 16B-16D illustrate, in one example, the formation of a back-side contact on the intermediate flow cell device of Figure 16A.

Figure 17A illustrates, in one example, a cross-sectional view of another intermediate flow cell device comprising multiple optical detection devices coupled within multiple cavities of a support frame, according to one or more aspects of the present invention.

Figures 17B and 17C illustrate, in one example, the formation of backside contacts on the intermediate flow cell apparatus of Figure 17A.

Figure 18A illustrates, in one example, a cross-sectional view of another intermediate flow cell device comprising multiple optical detection devices coupled within multiple cavities of a support frame, according to one or more aspects of the present invention.

Figures 18B and 18C illustrate, in one example, the formation of a back-side contact on the intermediate flow cell device of Figure 18A.

Figure 19A illustrates, in one example, a cross-sectional view of another intermediate flow cell device according to one or more aspects of the present invention, comprising a plurality of optical detection devices coupled within a plurality of cavities of a support frame.

Figures 19B and 19C illustrate, in one example, the formation of a back-side contact in the intermediate flow cell device of Figure 19A.

Figure 20 illustrates, in one example, a plurality of flow pools formed via the intermediate flow pool apparatus of Figure 19C according to one or more aspects of the present invention.

Figure 21 illustrates, in one example, the fluid channel and effective area of the optical detection device of Figure 20 with a flow cell according to one or more aspects of the present invention.

Figure 22 illustrates, in one example, multiple different flow cells that can be formed from the multiple flow cells of Figure 20 according to one or more aspects of the present invention.

Detailed Implementation

Various aspects of the invention, along with specific examples, features, advantages, and details thereof, are explained in more detail below with reference to the non-limiting examples shown in the accompanying drawings. Descriptions of known materials, construction tools, processing methods, etc., are omitted to avoid unnecessarily obscuring relevant details. However, it should be understood that the detailed descriptions and specific embodiments, while describing various aspects of the invention, are given by way of illustration only and not by way of limitation. Various substitutions, modifications, additions, and/or arrangements will be apparent to those skilled in the art within the spirit and/or scope of the inventive concept.

The approximate language used throughout this disclosure can be used to modify any quantitative expression that can be permissibly varied without causing a fundamental change in the associated function. Therefore, values modified by terms such as “about” or “substantially” are not limited to the specified exact values. For example, these terms can refer to less than or equal to ±5%, such as less than or equal to ±2%, such as less than or equal to ±1%, such as less than or equal to ±0.5%, such as less than or equal to ±0.2%, such as less than or equal to ±0.1%, such as less than or equal to ±0.05%. In some cases, the approximate language may correspond to the precision of the instrument measuring the value.

The terminology used herein is for the purpose of describing specific examples only and is not intended to be restrictive. Unless the context otherwise requires, the singular forms “a,” “an,” and “the” used herein are also intended to include the plural forms. Furthermore, references to “an example” are not intended to exclude the existence of other examples that also contain the described features. Additionally, unless explicitly stated otherwise, the terms “comprising” (and any form of “comprise,” such as “comprises” and “comprising”), “have” (and any form of “have,” such as “has” and “having”), “include” (and any form of “include,” such as “includes” and “including”), and “contain” (and any form of “contains,” such as “contains” and “containing”) are used as open-ended conjunctions. Any example of "including," "having," "comprising," or "containing" one or more steps or elements has one or more such steps or elements, but is not limited to having only one or more such steps or elements. As used herein, the terms "may" and "may be" indicate the possibility of occurrence in a set of circumstances; possessing a specified property, characteristic, or function; and/or defining the verb being modified by expressing one or more abilities, capabilities, or permissibility in relation to another verb. Thus, the use of "may" and "may be" indicates that the modified term is obviously appropriate, capable, or suitable for the expressed ability, function, or use, while also taking into account that in some cases the modified term may be inappropriate, incapable, or unsuitable. In some cases, an event or ability can be anticipated, while in others it cannot occur—this distinction is captured by the terms "may" and "may be."

As used herein, unless otherwise stated, the term "whole" (and any other form of "whole") means at least a majority, such as at least 95% or at least 99%. Therefore, unless otherwise stated, the term "whole" (and any other form of "whole") as used herein is not limited to 100%. As used herein, unless otherwise stated, the term "layer" is not limited to a single continuum of material. A "layer" can include multiple sublayers that may be the same or different materials, and/or may include coatings, adhesives, etc. Furthermore, one or more layers (or sublayers) of the flow cell disclosed herein may be modified (e.g., etched, deposited with material, etc.) to provide the functionality described herein.

The flow cell described herein can be used in a variety of biological or chemical processes and systems for academic or commercial analysis. More specifically, the flow cell described herein can be used in a variety of processes and systems where it is necessary to detect an event, property, quality, or characteristic as an indication of a specified reaction. For example, the flow cell described herein may include optical detection devices, biosensors and their components, and bioassay systems that operate with or are integrated with the aforementioned devices.

A flow cell can be configured to facilitate the detection of multiple designated reactions individually or jointly. The flow cell can be configured to perform multiple cycles in which multiple designated reactions occur in parallel. For example, a flow cell can be used to sequence dense DNA signatures through iterative cycles of enzyme manipulation and light or image detection/acquisition. Therefore, the flow cell can be coupled to one or more microfluidic channels that deliver reagents or other reaction components from the reaction solution to the reaction sites within the flow cell. Reaction sites can be provided or spaced in a predetermined manner, such as in a uniform or repetitive pattern. Alternatively, reaction sites can be randomly distributed. Each reaction site can be associated with one or more photoconductors and one or more photosensors that detect light from the associated reaction site. In some flow cells, reaction sites can be located in reaction recesses or reaction chambers that at least partially separate the designated reactions therein.

As used herein, a “designated reaction” includes a change in at least one of the chemical, electrical, physical, or optical properties (or mass) of a target chemical or biological substance (such as a target analyte). In a specific flow cell, a designated reaction is an active binding event, such as the binding of a fluorescently labeled biomolecule to a target analyte. More specifically, a designated reaction can be a chemical transformation, chemical change, or chemical interaction. A designated reaction can also be a change in electrical properties. In a specific flow cell, a designated reaction includes the binding of a fluorescently labeled molecule to an analyte. The analyte can be an oligonucleotide, and the fluorescently labeled molecule can be a nucleotide. A designated reaction can be detected when excitation light is directed to an oligonucleotide containing a fluorescent nucleotide, and the fluorophore emits a detectable fluorescent signal. In alternative flow cells, the detected fluorescence is the result of chemiluminescence or bioluminescence. A designated reaction can also, for example, increase fluorescence (or) resonance energy transfer (FRET) by bringing the donor fluorophore closer to the acceptor fluorophore, decrease FRET by separating the donor and acceptor fluorophores, increase fluorescence intensity by separating the quencher from the fluorophore, or decrease fluorescence by co-localizing the quencher and the fluorophore.

As used herein, “reaction solution,” “reaction component,” or “reactant” includes any substance that can be used to obtain at least one specified reaction. Possible reaction components include, for example, reagents, enzymes, samples, other biomolecules, and buffer solutions. Reaction components may be delivered to and/or immobilized at reaction sites in the flow cell disclosed herein. Reaction components may interact directly or indirectly with another substance, such as a target analyte immobilized at a reaction site in the flow cell.

As used herein, the term "reaction site" is a localized region where at least one specified reaction may occur. A reaction site may include a support surface of a reaction structure or substrate to which the substrate may be anchored. For example, a reaction site may include a surface of a reaction structure having reaction components (such as nucleic acid colonies) thereon (which may be located within a channel of a flow cell). In some flow cells, the nucleic acids in the clones have the same sequence; for example, they may be clone copies of single-stranded or double-stranded templates. However, in some flow cells, the reaction site may contain only a single nucleic acid molecule, for example, in single-stranded or double-stranded form.

Multiple reaction sites may be randomly distributed along the reaction structure of the flow cell, or they may be arranged in a predetermined manner (e.g., side-by-side in a matrix, such as a microarray). The reaction sites may also include reaction chambers or recesses that at least partially define spatial regions or volumes separating a specified reaction. As used herein, the terms "reaction chamber" or "reaction recess" include a spatial region of a defined support structure (which is typically in communication with a fluid channel). The reaction recess may be at least partially isolated from the surrounding environment or other spatial regions. For example, multiple reaction recesses may be separated from each other by a shared wall. As a more specific example, a reaction recess may be a nanopore formed by an indentation, pit, hole, groove, cavity, or recess defined by an inner surface of the detector surface, and has an opening or hole (i.e., an open structure) such that the nanopore is in fluid communication with a fluid channel.

In some flow cells, the reaction recesses of the flow cell's reaction structure can be sized and shaped to accommodate solids (including semi-solids), allowing the solid to be fully or partially inserted therein. For example, the reaction recesses can be sized and shaped to accommodate trapping microspheres. The trapping microspheres may have cloned and amplified DNA or other material on them. Alternatively, the reaction recesses can be sized and shaped to receive a suitable number of spheres or a solid substrate. As another example, the reaction recesses can be filled with porous gels or materials designed to control diffusion or filter fluids that may flow into the reaction recesses.

In a flow cell, one or more photodetectors (e.g., photodiodes) can be associated with corresponding reaction sites. When a specified reaction occurs at the associated reaction site, the photodetector associated with the reaction site detects light emission from that associated reaction site via at least one light guide. In some flow cells, multiple photodetectors (e.g., several pixels of a photodetector or camera) can be associated with a single reaction site. In other flow cells, a single photodetector (e.g., a single pixel) can be associated with a single reaction site or a group of reaction sites. The photodetectors, reaction sites, and other features of the flow cell can be configured such that at least some light is directly detected by the photodetectors without reflection.

As used herein, “biological or chemical substance” includes biomolecules, target samples, target analytes, and other compounds. Biological or chemical substances can be used to detect, identify, or analyze other compounds, or as intermediates for studying or analyzing other compounds. In a specific flow cell, biological or chemical substances include biomolecules. As used herein, “biomolecule” includes at least one of the following: biopolymers, nucleotides, nucleic acids, polynucleotides, oligonucleotides, proteins, enzymes, peptides, antibodies, antigens, ligands, receptors, polysaccharides, carbohydrates, polyphosphates, cells, tissues, organisms, fragments thereof, or any other biologically active compound (such as analogs or mimics of the above classes). In another example, biological or chemical substances or biomolecules include enzymes or reagents used in a coupled reaction to detect the product (such as an enzyme or reagent) of another reaction, such as enzymes or reagents used to detect pyrophosphate in a pyrosequencing reaction.

Biomolecules, samples, and biological or chemical substances may be natural or synthetic and may be suspended in a solution or mixture within a reaction depression or region. Biomolecules, samples, and biological or chemical substances may also be bound to a solid or gel material. Biomolecules, samples, and biological or chemical substances may also contain pharmaceutical compositions. In some cases, the target biomolecule, sample, and biological or chemical substance may be referred to as a target, probe, or analyte.

As used herein, a "flow cell" includes a cap extending above a reaction structure, the cap and the reaction structure forming a fluid channel therebetween, the fluid channel communicating with multiple reaction sites of the reaction structure; and includes at least one photodetector configured to detect a specified reaction occurring at or near the reaction site. The flow cell may include a solid-state photodetector or "imaging" device (e.g., a CCD or CMOS photodetector). As a specific example, the flow cell may be fluidly and electrically coupled to a cartridge with an integrated pump, the cartridge being fluidly and/or electrically coupled to a bioassay system. The cartridge and/or bioassay system may deliver reaction solutions to the reaction sites of the flow cell according to a predetermined protocol (e.g., synthetic sequencing) and perform multiple imaging events. For example, the cartridge and/or bioassay system may guide one or more reaction solutions along the reaction site via the fluid channel of the flow cell. At least one reaction solution may include four nucleotides having the same or different fluorescent labels. Nucleotides may bind to the reaction sites of the flow cell, such as corresponding oligonucleotides binding to the reaction sites. The cartridge and/or bioassay system can then use an excitation source (e.g., a solid-state source such as light-emitting diodes (LEDs)) to cause the reaction site to emit light. The excitation source may have a predetermined wavelength or multiple wavelengths, including a wavelength range. The fluorescent label excited by the incident excitation light can provide an emission signal (e.g., light with one or more wavelengths that are different from and may be different from each other) that can be detected by the photosensor of the flow cell.

The disclosed flow cell can be configured for physical or chemical analysis to obtain any related information or data. A specific flow cell may include portions of a nucleic acid sequencing system (or sequencer) configured for various applications, including but not limited to de novo sequencing, whole-genome or target gene region resequencing, and metagenomics. The sequencing system may be configured to perform DNA or RNA analysis. The flow cell may be configured to perform a large number of parallel reactions on its effective surface to obtain reaction-related information.

A flow cell may include one or more fluid channels that guide the solution to reaction sites on an effective region/surface of a reaction structure above one or more photodetectors, as will be further explained below. Therefore, in use, the flow cell may be in fluid communication with, for example, a fluid storage system (not shown) that can store various reaction components or reactants used to carry out a specified reaction in the flow cell. The fluid storage system may also store fluids for washing or cleaning one or more fluid channels of the flow cell and/or diluting reactants. For example, the fluid storage system may include multiple reservoirs for storing samples, reagents, enzymes, other biomolecules, buffer solutions, aqueous solutions, and nonpolar solutions, etc. Furthermore, the fluid storage system may include a waste reservoir for receiving waste products from the flow cell.

Figure 1 illustrates an example of a photodetector 10 that can be used in the flow cell of the present invention. The photodetector 10 may include multiple stacked layers (such as a base layer or wafer 14) and multiple dielectric layers, as well as a metal dielectric layer extending thereon. As shown in Figure 1, the photodetector 10 includes a sensor array of photosensors 12 and a photoguide array of photoguides 18. The photodetector 10 may also include a reaction structure 20 extending along a top portion 20 of the photodetector 10 (including above the openings of the photoguides 18). The photodetector 10 may be configured such that each photosensor 12 corresponds to or aligns with a single photoguide 18 and/or a single reaction recess 16 (e.g., a nanopore) of the reaction structure 20 located above the upper surface 22 of the photodetector 10, so that it receives photons only therefrom. However, in other examples, a single photosensor 12 may receive photons through more than one photoguide 18 and/or from more than one reaction recess 16. A single photosensor 12 may thus form one or more pixels. As shown in Figure 1, the reaction depression 16 can be defined by, for example, a dent or a variation in depth (or thickness) in the upper surface of the reaction structure 20.

As shown in Figure 1, the array of optical waveguides 18 and reactive recesses 16 of the reactive structure 20 (and the potential photosensitive sensor 12) can be provided in a defined repeating pattern, such that at least some of the recesses 16 and/or waveguides 18 (and the potential photosensitive sensor 12) are equally spaced from each other in the defined positional pattern. In other examples, the reactive recesses 16 and/or waveguides 18 (and the potential photosensitive sensor 12) can be provided in a random pattern, and/or at least some of the reactive recesses 16 and/or waveguides 18 (and the potential photosensitive sensor 12) can be variably spaced from each other. The gap regions between the arrays of reactive recesses 16 can be substantially planar. As further explained below, the array of reactive recesses 16 of the reactive structure 20 can have at least one corresponding reactive site provided therein (e.g., fixed to its surface).

The photosensitizing region of the photodetector 10 is referred to as the effective region of the device 10. Therefore, the effective region of the photodetector 10 includes a region containing a light guide 18 that directs light toward the photosensor 12. The upper surface 22 of the photodetector 10 may include a reaction structure 20 having a row of reaction recesses 16, each having at least one corresponding reaction site on/within which it can be used for reagent delivery and reaction (e.g., reaction to an analyte in a reaction solution) and illumination during flow cell operation. As shown in FIG1, the reaction structure 20 may extend over the entire (e.g., at least 96%, or at least 99%, or 100%) effective region of the photodetector 10. In such a configuration, the upper surface or detector surface of the reaction structure 20 may define the effective surface of the photodetector 10 over which the reaction solution can flow and interact with the reaction sites formed on/within the reaction recesses 16. The effective surface of the photodetector 10 may include the surfaces of the recesses 16 and gap regions extending between and around the recesses 16.

The exposed upper surface of the reaction structure 20 (i.e., the exposed upper surface of the reaction recess 16 and/or the gap region extending therebetween and around it) may include a smooth, planar/flat surface. In certain examples, the gap region of the exposed upper surface of the reaction structure 20 and/or the exposed upper surface of the reaction recess 16 may be a smooth, planar/flat surface, which prevents the reaction solution or any other biological or chemical substance from being trapped or retained thereon and/or prevents pad hopping errors. For example, the exposed upper surface of the reaction structure 20 may include a surface roughness micrometer range, such as less than or equal to 20 μm, or less than or equal to 1 μm. In some examples, the reaction structure 20 may include a surface roughness less than or equal to 100 nm, or less than or equal to 10 nm.

The reaction structure 20 may include one or more layers. In one example, the reaction structure 20 includes multiple overlapping layers. The reaction structure 20 may include one or more layers configured to allow excitation light signals and/or emitted light signals from reaction sites in the reaction recess 16 (after treatment with the reaction solution) to pass through therethrough, into openings of one or more corresponding light guides 18, and potentially connected to one or more corresponding photosensors 12 (e.g., depending on the configuration of the light guides 18). As another example, the reaction structure 20 may include more than one layer that may include layers that prevent crosstalk or “sharing” propagation or transmission of emitted light from specific reaction sites in the reaction recess 16 to non-corresponding sensors 12. The reaction structure 20 may provide a solid that allows the immobilization of target chemicals, biomolecules, or other analytes thereon. For example, each reaction site on the reaction recess 16 may include a cluster of biomolecules immobilized on its exposed outer surface. Thus, the reaction structure 20 may include a material that allows the immobilization of reaction sites onto the reaction recess 16. The reaction structure 20 may be physically or chemically modified to facilitate the immobilization of biomolecules to form reaction sites and/or to facilitate the detection of their light emission. Examples of layers that can form the reactive structure 20 include at least one SiN layer and at least one TaO layer. However, the reactive structure 20 may include different layers (e.g., different layers, fewer layers, and/or additional layers) and/or different materials.

The light guide 18 may include a filter material configured to filter excitation light or a wavelength range containing the wavelength of the excitation light, and allow light emission (or a wavelength range containing the light emission) from at least one reaction site of at least one corresponding reaction recess 16 to pass through and propagate toward at least one corresponding photosensor 12. The light guide 18 may be an absorption filter (e.g., an organic absorption filter) such that the filter material absorbs a specific wavelength (or wavelength range) and allows at least one predetermined wavelength (or wavelength range) to pass through it. Each of the light guides 18 in the array may include substantially the same filter material, or different light guides 18 may include different filter materials. Thus, each light guide 18 may be positioned relative to the surrounding material (e.g., a dielectric material) of the device 10 to form a light guide structure. For example, the light guide 18 may have a refractive index of at least about 20. In some configurations, the light guide 18 may be configured such that the optical density (OD) or absorbance of the excitation light is at least about 4OD.

As shown in Figure 1, the photodetector 10 may include circuitry 24 for transmitting or conducting signals when the photosensor 12 detects light emission (e.g., photons). As discussed above, light emission may originate from or be associated with at least one reaction site of the reaction recess 16 of the reaction structure 20, and be guided or directed by at least one light guide 18 into the associated photosensor 12. Circuitry 24 may include interconnected conductive elements (e.g., conductors, traces, vias, interconnects, etc.) capable of conducting current, such as transmitting data signals based on detected photons. For example, circuitry 24 may resemble or include a microcircuit device. The photodetector 10 may include at least one integrated circuit having an array of photosensors 12 electrically coupled to circuitry 24. Circuitry 24 within the photodetector 10 may be configured for at least one of signal amplification, digitization, storage, and processing. Circuitry 24 may collect (and potentially analyze) the light emission detected by the sensor 12 and generate data signals for communicating the detection data with a bioassay system. Circuitry 24 may also perform additional analog and/or data signal processing within the photodetector 10.

As shown in FIG1, the device circuit 24 of the photodetector 10 may extend to the vicinity of or only partially through the base portion 14. Therefore, the base portion 14 may be a cavity for conductive vias or other portions of the device circuit 24 extending therethrough. The back side 26 of the base portion 14 may form an exposed back surface 26 of the photodetector 10, which may be a cavity of the device circuit 24. In other words, the device circuit 24 may be completely positioned above the back side 26 of the base portion 14 within the photodetector 10, such that the device circuit 24 is inaccessible at the back side 26 of the base portion 14 and/or the device 10 itself. However, as shown in FIG1, the device circuit 24 may extend to the top side of the photodetector 10. For example, the device circuit 24 may extend through the photodetector 10 to and potentially through the reactive structure 20. Therefore, the top side of the photodetector 10, which may be formed by the exposed upper surface of the reactive structure 20 (if present), may include the device circuit 24, as shown in FIG1. In other words, the device circuit 24 may be exposed and accessible on the top side of the photodetector 10 (which may be the top side of the reaction structure 20, if present), as shown in Figure 1.

Photodetector devices can be manufactured using integrated circuit manufacturing processes, such as those used to manufacture charge-coupled device (CCD) circuits or complementary metal-oxide-semiconductor (CMOS) devices or circuits. Therefore, photodetector devices can include, for example, one or more semiconductor materials, and can take the form of, for example, a CMOS photodetector device (e.g., a CMOS image sensor) or a CCD sensor (another type of image sensor). As shown in FIG1, in an embodiment of this application, photodetector 10 is a CMOS-type image sensor, but other types of sensors can also be used. For example, as shown in FIG1, photodetector 10 can be semiconductor-based and includes multiple stacked layers comprising a device base portion 14 (which can be, for example, a silicon layer or a wafer).

When configured as a CMOS-type photodetector 10, the "complementary" aspect refers to the simultaneous inclusion of n-type and p-type metal-oxide-semiconductor field-effect transistors (MOSFETs) in an integrated circuit (IC) constructed using CMOS technology. Each MOSFET has a metal gate with a gate electrolyte (such as oxide) (hence the "metal-oxide" part in its name) and a semiconductor material located beneath the gate (corresponding to the "semiconductor" in its name). When the photodetector 10 is configured as shown in FIG1, the photosensor 12 can be electrically coupled to the circuit 24 via, for example, its gate.

For a semiconductor-based photodetector 10, at least some circuits 24 may be disposed within a device or substrate layer, and light guides 18 may each extend through the device or substrate layer. Each substrate layer may include interconnected conductive elements forming at least a portion of the device circuits 24, with dielectric material surrounding or adjacent to the conductive elements of the circuits. Thus, the conductive elements of the circuits 24 may be embedded within the dielectric material. The light guides 18 may also extend through the dielectric material and may be spaced apart from the circuits. Various metallic elements and/or dielectric materials may be used, such as those suitable for integrated circuit fabrication (e.g., CMOS fabrication). For example, the conductive elements/circuits 24 may be metallic elements such as W (tungsten) elements, Cu (copper) elements, Al (aluminum) elements, or combinations thereof, but it should be understood that other materials and structures may also be used. The dielectric material may be a low-k material and/or a silicon-containing material, such as _SiO2 , but it should be understood that other dielectric materials and structures may also be used.

The photodetector 10 can be an integrated circuit chip. For example, the photodetector 10 can be manufactured as a large number of photodetectors 10 provided on a single base part (e.g., a wafer) of electronic-grade silicon (EGS) or other semiconductors (such as GaAs). Thus, multiple such manufactured devices can be integral and formed/arranged adjacently and positioned very close to each other. The wafer is cut (i.e., sliced) into many pieces, each containing at least one different photodetector 10. As shown in FIG1, a single different photodetector 10 can be formed (i.e., sliced) from multiple integral wafer devices thus formed. Alternatively, multiple integrated adjacent photodetectors 10 can be formed (i.e., sliced) from multiple integrated wafer devices thus formed.

Figure 1 illustrates another example of a photodetector 110 that can be used in the flow cell of the present invention. The photodetector 110 of Figure 2 is similar to the photodetector 10 of Figure 1; therefore, similar figures beginning with "1" are used to denote similar components, aspects, functions, methods, or features, to which the above description also applies, and will not be repeated for the sake of brevity and clarity. As shown in Figure 2, the difference between the photodetector 110 and the photodetector 10 is that the photodetector 110 does not include a reaction structure (forming a reaction recess and a gap region extending therein and around it) positioned above its upper surface 122. Instead, the manufactured or cut photodetector 110 may not contain a reaction structure. A reaction structure may be positioned on the upper surface 122 of the cut photodetector 110, for example, after processing the photodetector 110 as further explained below.

The difference between the photodetector 110 and the photodetector 10 lies in that the circuit 124 includes a via 128 that extends completely through the base wafer portion 114, as shown in FIG2. Therefore, the via 128 is exposed and accessible on the back side 126 of both the base wafer portion 114 and the device 110 itself. Also as shown in FIG2, the back side 126 of the base wafer portion 114 (and the device 110 itself) includes one or more spacer portions 130 extending from the back side 126 of the base wafer portion 114. At least one spacer portion 130 may be spaced apart from, located near, or only partially overlapped with the via 128 on the back side 126 of the base wafer portion 114. Thus, at least one spacer portion 130 can be positioned on the back side 126 of the base wafer portion 114 such that at least a portion of each via 128 is exposed and usable on the back side 126 of both the base wafer portion 114 and the device 110 itself. As shown in FIG2, the photodetector 110 may include at least two spacer portions 130 extending along opposite sides of the back side 126 of the base wafer portion 114. At least one spacer portion 130 may provide structural support or rigidity to the base wafer portion 114, thus protecting the device 10 itself (which may be affected by or weakened by the via 128). In some photodetectors 110, at least one spacer portion 130 may be electrically insulating or non-conductive (or semiconductor) to avoid interfering with the operation of the sensor 112 and/or circuitry 124, for example. Exemplary materials forming at least one spacer portion 130 include, but are not limited to, glass, quartz glass, crystal, silicon, fiberglass, plastics, epoxy resins, ceramics, dielectric composites, paper, or combinations thereof.

As shown in Figures 3-5, a support structure 32 comprising a support frame 34 and a support substrate 44 can be used to form the flow pool of the present invention. The support frame 34 may define an upper surface 36, a lower surface 38, and at least one cavity 40 (e.g., a gap or hole) extending through the frame 34 between the upper and lower surfaces 36/38. The support structure 32 may include any number of cavities 44. As shown in Figures 3 and 4, the support frame 34 may include a plurality of different arrays of spaced cavities 40. The arrays of cavities 40 may be spaced apart from each other such that a portion of the support frame 34 extends entirely around each cavity 40, thus situated between adjacent cavities 40. The arrays of cavities 40 may be defined by a repeating (possibly uniform) pattern such that the cavities 40 are uniformly or consistently spaced. Alternatively, the arrays of cavities 40 may be randomly distributed such that at least some cavities 40 are non-uniformly spaced. As shown in Figure 5, each cavity 40 may be formed by an inner sidewall 50 of the support frame 34 extending between the upper and lower surfaces 36, 38. In some configurations, the inner wall 50 of the support frame 34 defining the cavity 40 may extend vertically between the upper and lower surfaces 36, 38, such that the cavity 40 may be defined with the same size and shape at the upper surface 36 and the lower surface 38.

Each cavity 40 may be sized and shaped to include one or more photodetectors, such as the photodetector 110 of FIG2 described above, as shown in FIG4 and 5. However, as further explained below, one or more photodetectors of different structures may be used within the cavities 40 of the support frame 34, for example, but not limited to, the photodetector 10 of FIG1 described above. Furthermore, at least one photodetector of a first structure may be used in one or more first cavities 40 of the support frame 34, and at least one photodetector of a second structure may be used in one or more second cavities 40 of the support frame 34.

The support frame 34 may be substantially planar. For example, the upper surface 36 and/or lower surface 38 of the support frame 34 may be planar and parallel. In some configurations, the upper surface 36 and/or lower surface 38 may be substantially smooth, such as having a surface roughness on the submicron scale. In some configurations, the upper surface 36 and/or lower surface 38 may include a surface roughness of less than or equal to 50 nm or less than or equal to 10 nm. In some examples, the upper surface 36 and/or lower surface 38 may include a surface roughness in the range of 1-2 nm. As further explained below, the upper surface 36 of the support frame 34 may cooperate with the detector surface (e.g., the effective surface of the device) of the reaction structure of the photodetector to form a flow cell path for delivering a reagent solution, or the reaction structure, one or more other layers and/or cap may be positioned above the upper surface 36 of the support frame 34 and the upper portion 122 of the photodetector. Therefore, the flatness/smoothness of the upper surface 36 of the support frame 34 (and the upper surface of the reaction structure) may be configured to allow the reagent fluid flow to proceed without entraining or trapping fluid.

The support frame 34 and the potential substrate 44 can be relatively rigid to securely hold and couple the photodetector 110 within the cavity 40 and prevent destructive twisting/deformation of the photodetector 110 during the manufacture, processing, and/or use of the flow cell of the present invention. In some configurations, the support frame 34 (and the possible substrate 44) has a Young's modulus of at least 50 GPa or at least 70 GPa. In some configurations, the coefficient of thermal expansion (CTE) of the support frame 34 (and the possible substrate 44) can be at least about 20/°C or at least about 30/°C. For example, the support frame 34 can comprise borosilicate glass (e.g., Eagle glass) with a Young's modulus in the range of 70-80 GPa and a CTE in the range of 30-35/°C, or it can be composed of silicon with a Young's modulus in the range of 160-170 GPa and a CTE in the range of 35-40/°C.

During the formation of reaction sites on the reaction structure positioned above the upper portion 122 of the photodetector 110, the support frame 34 may be brought into contact with reagent solutions and/or other materials/solutions. The support frame 34 may comprise one or more materials that do not react with sequencing reagents (such as sequencing reagents used for DNA grafting, aggregation, cutting, synthesis, and/or reading). For example, the sequencing solution may be an aqueous solution and/or may consist of oil.

During the formation of one or more flow pools, the support frame 34 may undergo a chemical mechanical polishing (CMP) process, as further explained below. The support frame 34 may include one or more materials that do not react with the CMP slurry and mixture that comes into contact with it during the formation of the one or more flow pools. For example, the CMP slurry or mixture may include abrasive particles and a base liquid. In some examples, the base liquid may include water (e.g., deionized water) and/or oil. In some examples, the abrasive particles may include oxides, such as silica, cerium dioxide, and/or alumina.

The support frame 34 can electrically insulate at least one photodetector 110 positioned within each cavity 40 so as not to interfere with its photosensitive operation. At least a portion of the thickness/cross-section of the portion supporting the support frame 34 surrounding/forming the cavity 40 (extending between the upper and lower surfaces 36, 38) may include an electrically insulating (i.e., non-conductive) material (or a semiconductor material). For example, at least a portion of the thickness/cross-section of the portion surrounding/forming the cavity 40 extending from the upper surface 36, or the intermediate portion separating the upper and lower surfaces 36, 38, may include an electrically insulating (i.e., non-conductive) material (or a semiconductor material). In some configurations, the support frame 34 may consist only of electrically insulating material. Exemplary electrical insulating materials that can form at least a portion of the support frame include silicon, glass (e.g., crystal, quartz glass, glass fiber, borosilicate glass (e.g., alkaline earth metal borosilicate glass, such as Eagle glass), float borosilicate glass (e.g., 33 glass) or other low self-fluorescence glass), ceramics, polymers (e.g., plastics, epoxy resins, silicon charged epoxy resins or UV-cured epoxy resins or adhesives), dielectric composites, paper, or combinations thereof.

However, as further explained below, a portion of the support frame 34 may include a conductive material, such as a metallic material. For example, as further explained below, the support frame 34 may include a conductive via extending through a portion of the thickness/cross-section of the support frame 34 adjacent to (e.g., adjacent to) a cavity 40 extending between (and exposed at) the upper and lower surfaces 36, 38. In some configurations, a portion of the thickness/cross-section of the support frame 34 surrounding/forming the cavity 40 extending from the upper surface 36 and/or the lower surface 34 may include a conductive material (which may include a portion of the via).

The support frame 34 may include a plurality of visual indicators/markers 45, as shown in FIG4. The visual indicators 45 may be used to reference the position and/or orientation of the support frame 34 as a whole and/or a portion thereof, or components coupled thereto (such as, for example, cavity 40 and one or more photodetectors 110 positioned within cavity 40, as further explained below). Thus, the visual indicators 45 may serve as alignment marks during the processing of the support frame 34 (and its coupled components, as further explained below) into one or more intermediate flow cell devices and/or flow cell devices (as further explained below). For example, the visual indicators 45 may be used for alignment during capping and/or cutting operations to form one or more intermediate flow cell devices and/or flow cell devices.

Visual indicator 45 may include any material that is visually different from the support frame 34 relative to the human eye and/or imaging device (e.g., a digital camera). In some examples, visual indicator 45 may include pigments, paints, dyes, luminescent materials, metals, oxides, or combinations thereof. Visual indicator 45 may include one or more materials that do not react with sequencing reagents and/or CMP slurry.

The visual indicator 45 may be disposed on the lower surface 38 of the support frame 34 (as shown in FIG. 4), on the upper surface 36 of the support frame 34, at least partially embedded within the thickness of the support frame 34 between the upper and lower surfaces 36, 38, or a combination thereof. The visual indicator 45 may be formed on the support frame 34 by any method. In some examples, the visual indicator 45 may be formed on the support frame 34 by printing methods such as spraying or lithography.

As shown in Figures 4 and 5, the support structure 32 may include the upper surface 36 of a support frame 34 coupled to the upper surface 46 of the substrate or carrier 44. The support frame 34 and the substrate 44 may be removably coupled or fixedly coupled. In some support structures 32, the substrate 44 may be composed of the same or similar material as the support frame 34. In some other support structures 32, the substrate 44 may be composed of a different material than the support frame 34. The upper surface 46 of the substrate 44 may be substantially smooth and planar, such that the upper surface 36 of the support frame 34 is parallel to and may be substantially coplanar with the upper surface 46 of the substrate 44, as shown in Figure 5. In some structures, the upper surface 46 of the substrate 44 may define a surface smoothness that is the same as or similar to that of the upper surface 36 of the support frame 34.

As also shown in Figures 4 and 5, for the upper surface 3 of the support frame 34 coupled to the upper surface 46 of the substrate 44, at least one dicing light detection device 110 can be positioned "face down" within the cavity 40, such that the upper surface 122 of at least one light detection device 110 is positioned on or adjacent to the upper surface 46 of the substrate 44. Thus, the upper surface 122 of at least one light detection device can be substantially aligned with (e.g., coplanar) the upper surface 36 of the support frame 34. Similarly, if at least one dicing light detection device 110 includes a reaction structure provided above the upper surface 122 (e.g., as with the light detection device 10 of Figure 1), the effective surface of the detector's upper surface/reaction structure can be positioned on or adjacent to the upper surface 46 of the substrate 44, and the gap portion can be substantially aligned with (e.g., coplanar) the upper surface 36 of the support frame 34.

As shown in FIG. 5, the support frame 34 may be thinner than at least one photodetector 110, such that its back side 126 extends through the lower surface 38 of the support frame 34. In some other support frame 34 configurations, the lower surface 38 of the support frame 34 may be flush with or below the back side 126 of at least one photodetector 110. At least one photodetector 110 may define a correspondingly smaller size compared to the cavity 40. Thus, cutting at least one photodetector 110 may position it within the cavity 40 of the support structure 32 such that the outer periphery of at least one photodetector 110 is spaced apart from the inner sidewall 50 of the support frame 34, as shown in FIG. 5. For example, a portion of the cavity 40 may extend around the periphery of at least one photodetector 110 to form a groove or edge cavity portion 52 supporting the cavity 40 of the support frame 34 and the periphery of at least one photodetector 110.

At least one photodetector 110 may be freely located directly on the upper surface 46 of the substrate 44 within the cavity 40. In some such arrangements, at least one photodetector 110 may be mechanically held within the cavity 40 by means of tools or support members.

Figure 6 illustrates a support structure 232 according to another example of the invention. The support structure 232 of Figure 6 is similar to the support structure 32 of Figures 3-5; therefore, similar reference numerals beginning with “2” are used to denote similar components, aspects, functions, processes, or features, and the descriptions relating to it above also apply, and will not be repeated for the sake of brevity and clarity. As shown in Figure 6, the support structure 232 differs from the support structure 32 which includes an interposer member or layer 248 in that it chemically couples/bonds the upper portion 122 of at least one photodetector 210 to the upper surface 246 of the substrate 244 within the cavity 244. The interposer 248 can be any temporary or removable bonding material (e.g., via one or more chemical, mechanical, and/or irradiation processes). In one example, the interposer 248 may comprise a polymeric material (e.g., one or more cyclic olefin copolymers) which may be provided in a solvent-cast bonding material composition. For example, the interposer 248 may comprise temporary bonding materials such as 220 or 305 sold by Brewer Science, Inc. In another example, the interposer 248 may include a high UV absorption release layer and/or an adhesive layer, such as the JSRELPAC TA series temporary bonding materials sold by JSR Corporation. The interposer 248 may be formed by spin coating, spraying, dye slot coating, or lamination onto the upper surface 246 of the substrate 244.

Intermediate layer 248 may include one or more material layers extending over the upper surface 246 of substrate 244 within cavity 240. Therefore, the upper portion 122 of at least one photodetector 110 may be located on the upper surface 247 of intermediate layer 248 within cavity 244. Intermediate layer 248 may also extend between the upper surface 246 of substrate 244 and the upper surface 236 of support frame 234, as shown in FIG6. Therefore, the top side 236 of support frame may extend over the upper surface 247 of intermediate layer 248, and intermediate layer 248 may extend over the top side 246 of substrate 244.

Figure 7 illustrates a support structure according to another example of the invention. The support structure 332 of Figure 7 is similar to the support structure 32 of Figures 3-5 and the support structure 232 of Figure 6; therefore, similar reference numerals beginning with "3" are used to denote similar components, aspects, functions, processes, or features, and the descriptions relating to them above also apply, and will not be repeated for the sake of brevity and clarity. As shown in Figure 7, the support structure 332 differs from support structures 32 and 232 in that it includes a spacer member/layer 349 that separates the upper surface 346 of the substrate 344 from the upper portion 122 of at least one photodetector 110. The spacer layer 349 may extend only between the upper surface 346 of the substrate 344 and the upper surface 336 of the support frame 334, and therefore will not extend through the cavity 340. In this manner, the spacer layer 349 lifts the upper surface 336 of the support frame 334 from the upper surface 346 of the substrate 344, wherein the upper portion 122 of at least one photodetector 110 covers the surface 346 of the substrate 344. Thus, the spacer layer 349 spaces the upper portion 122 of at least one photodetector 110 from the upper surface 336 of the support frame 224 (i.e., above it) in a direction extending from the back side 126 to the upper portion 122 of at least one photodetector 110. The spacer layer 349 may comprise the same or similar material as the interposer layer 248. The spacer layer 349 may be formed by spin coating, spraying, dye slot coating, or lamination. Although the support structure 332 of FIG. 7 is shown without an interposer layer (e.g., the interposer layer 248 of the support structure 232 of FIG. 6), the support structure 332 may comprise an interposer layer extending above the upper surface 346 of the substrate 344 between the substrate 344 and the support frame 334 and across the cavity 340.

Figure 8 shows a support structure 432 according to another example of the invention. The support structure 432 of Figure 8 is similar to the support structure 32 of Figures 3-5, the support structure 232 of Figure 6, and the support structure 332 of Figure 7; therefore, similar reference numerals beginning with "4" denote similar components, aspects, functions, processes, or features, and the descriptions relating to them above also apply, and will not be repeated for the sake of brevity and clarity. As shown in Figure 8, the difference between support structure 432 and support structures 32, 232, and 332 lies in the structure of the sidewall 450 of the cavity 440.

As shown in Figure 8, each cavity 440 may be formed by an inner wall 450 of a support frame 434 extending between upper and lower surfaces 436, 438. When the inner wall 450 of the support frame 434 defining the cavity 440 extends from the lower surface 438 to the upper surface 436, it may extend inward into the interior of the cavity 440 such that the size of the cavity 44 at the upper surface 436 is smaller or narrower than that at the lower surface 438 (i.e., the opening of each cavity 440 at the lower surface 438 is larger than its opening at the upper surface 436). It should be noted that at the upper surface 436, the sidewall 450 may extend very close to, but still spaced from, the outer periphery of at least one photodetector 110. Accordingly, the edge cavity portion 452 of the cavity 440 extending between the inner wall 450 and the outer periphery of at least one photodetector 110 may narrow as it extends from the lower surface 438 to the upper surface 436.

The shape or structure of the inner sidewall 450 may be formed by any structure of the support frame 434 and/or by manufacturing or processing techniques. For example, the support frame 434 may comprise multiple support frame layers with openings of different sizes, so that when stacked and coupled together, the openings form a cavity 40. As another example, the shape or structure of the inner sidewall 450 may be formed by etching or otherwise shaping or forming the support frame 434.

In one example, the inner wall 450 may extend linearly (i.e., planar) inward toward the interior of the cavity 440 from the upper surface 436 to the lower surface 434, as shown in Figure 8. In other examples, the inner wall 450 may not extend linearly (i.e., planar). For example, the inner wall 450 may extend linearly, curvilinearly, or a combination thereof from the lower surface 438 to the upper surface 436, such that the size of the cavity 440 is smaller or narrower at the upper surface 436 compared to the lower surface 438. In one such example, a portion of the inner wall 450 of the support frame 534 defining the cavity 440 may extend perpendicularly from the lower surface 438 to the upper surface 436 along a portion of the thickness of the support frame 534, and another portion may extend linearly (i.e., an angled plane) from it inward toward the interior of the cavity 540 to the upper surface 436.

Figures 9-11B illustrate how individual photodetectors 110 are coupled via support/fill material 60 to each cavity 40 of the support frame 34 of the support structure 32 of Figures 3-5. As shown in Figure 9, the support material 60 can be introduced from an exposed side adjacent to the lower surface 38 of the support frame 34 into the edge cavity portion 52 between the sidewall 50 of the support frame 34 and the outer periphery of the photodetector 110. The support material 60 can securely couple the support frame 34 and the photodetector 110 together. Specifically, as shown in Figures 11A and 11B, the support material 60 can extend around the outer periphery of the side of the photodetector 110 positioned within the cavity 40. Thus, the support material 60 can extend between the outer periphery of the side of the photodetector positioned within the cavity 40 and the sidewall 50 of the cavity 40 and couple them together. In some examples, after the support material 60 is disposed within each cavity 40, the lower surface 38 of the support frame 34, the support material 60, and/or the photodetector 110 within each cavity 40 may undergo one or more CMP operations. For example, the support material 60 and/or the photodetector 110 within at least one cavity 40 may extend at least above (i.e., above) the adjacent portion of the lower surface 38 of the support frame 34, and one or more CMP operations may remove a portion of the support material 60 and/or the photodetector 110 to flatten the lower surface 38 of the support frame 34, the support material 60, and the photodetector 110.

The support material 60 can be any processed material (e.g., in a first state, such as liquid or powder) capable of flowing into or otherwise introducing into the edge cavity portion 52, and securely couples the support frame 34 and the photodetector 110 within the cavity 40 together (e.g., in a second state, such as hardened or cured). The support material 60 can be electrically insulating or non-conductive (or semiconductor) so as not to interfere with the operation of the photodetector 110 (e.g., the operation of sensor 112 and/or circuitry 124). During the formation of the reaction structure of the flow cell of the present invention, the formation of reaction sites on the reaction structure, luminescence/detection, and/or preparation or cleaning, the support material 60 may be contacted with reagent solutions and/or other materials/solutions. Therefore, the support material 60 may include one or more materials that do not react with sequencing reagents (e.g., sequencing reagents for DNA grafting, aggregation, cutting, synthesis, and/or reading). For example, sequencing reagents may include water and/or oil. Exemplary materials for the support material 60 include silicon, glass (e.g., crystal, quartz glass, glass fiber, borosilicate glass (e.g., alkaline earth borosilicate glass, such as Eagle glass), float borosilicate glass (e.g., 33 glass) or other low self-fluorescence glass), ceramics, polymers (e.g., plastics, epoxy resins, silicone-charged epoxy resins or UV-cured epoxy resins or adhesives), dielectric composites or combinations thereof.

As shown in Figures 10-11B, after the support material 60 fills the edge cavity portion 52 and securely couples the support frame 34 and at least one photodetector 110 to at least one cavity 40, the remaining portion of the support structure 32 can be removed. For example, the substrate 44 and any associated interlayers and/or spacers/components can be removed from the upper surface 36 of the support frame 34, the upper portion 122 of the photodetector 110, and the upper surface of the support material 60, as shown in Figure 10. The separated support frame 34, the at least one photodetector 110 positioned within at least one cavity 40, and the disposed support material 60 may include an intermediate flow cell device 62, as shown in Figures 11A and 11B. The intermediate flow cell device 62 can be further processed into one or more flow cells, as further explained below. As described above, although the optical detection device 110 of FIG2 is illustrated with an array of cavities 40 in the support frame 34 of the intermediate flow cell device 62 of FIG9-11B, optical detection devices with other structures as shown in FIG1 can be similarly or equally used in at least one cavity 40 of the support frame 34.

The manner or method of removing the intermediate flow cell device 62 from the rest of the support structure 32 may be at least partially related to the support frame 34 and the substrate 44 (and/or any associated intermediaries and/or spacers/members) and/or their attachment. In some configurations, the intermediate flow cell device 62 may be debonded from the rest of the support structure 32. In some configurations, the substrate 44 and any associated intermediaries and/or spacers/members (if present) may be chemically and/or mechanically etched off the intermediate flow cell device 62. In some configurations, the substrate 44 and any associated intermediaries and/or spacers/members (if present) may be removed from the intermediate flow cell device 62 via, for example, blowering, blade insertion, vacuum debonding, or mechanical lifting with or without pretreatment (such as edge trimming or laser patterning).

As shown in Figures 9-11B, in some configurations, individual photodetectors 110 may be positioned within at least one cavity 40 of the support frame 34. As described above and as shown in Figures 9-11B, in such configurations, support material 60 may be disposed within an edge cavity portion 52 between the sidewall 50 of the support frame 34 and the outer periphery of the individual photodetectors 110 within each cavity 40, to couple the support frame 34 and the individual photodetectors 110 together.

As shown in Figures 12A and 12B, in some other configurations of the intermediate flow cell device 662, a plurality of spaced-apart photodetectors 110A, 110B, 110C may be positioned within at least one cavity 640 of the support frame 634. It should be noted that although three photodetectors 110A, 110B, 110C are used herein to illustrate the use of multiple photodetectors, any number of photodetectors (e.g., two, three, four, five, etc.) can also be used. The intermediate flow cell device 662 of Figures 12A and 12B is similar to the intermediate flow cell device 62 of Figures 11A and 11B; therefore, similar reference numerals beginning with “6” instead of “1” are used to denote similar components, aspects, functions, processes, or features, and the descriptions relating to them above also apply, and will not be repeated for the sake of brevity and clarity.

As shown in Figures 12A and 12B, in the intermediate flow pool device 662 of this type of structure, the support material 660 can be disposed within the edge cavity portion 652 between the sidewall 650 of the support frame 634 and the outer peripheral sides of a plurality of spaced-apart different photodetectors 110A, 110B, 110C adjacent to and/or facing it, so as to couple the support frame 634 and the photodetectors 110A, 110B, 110C together. Furthermore, as shown in Figures 12A and 12B, the different photodetectors 110A, 110B, 110C can be spaced apart from each other, such that the internal device portion 653 of the gap or cavity 640 is positioned between adjacent different photodetectors 110A, 110B, 110C. The support material 660 can be positioned within the gap portion 652 between adjacent different photodetectors 110A, 110B, 110C to couple the devices 110A, 110B, 110C together and to the support frame 634. In this way, the support material 660 can extend to the periphery of the photodetectors 110A, 110B, and 110C located at different intervals within the cavity 640.

As shown in Figures 13A and 13B, in some other configurations of the intermediate flow cell device 762, multiple integral, coupled, or unseparated different photodetectors 110A, 110B, 110C may be positioned within at least one cavity 740 of the support frame 734. The intermediate flow cell device 762 of Figures 13A and 13B is similar to the intermediate flow cell device 62 of Figures 11A and 11B and the intermediate flow cell device 662 of Figures 12A and 12B; therefore, similar reference numerals beginning with “7” instead of “1” or “6” are used to denote similar components, aspects, functions, processes, or features, and the descriptions relating to them above also apply, and will not be repeated for the sake of brevity and clarity.

As shown in Figures 13A and 13B, in this type of intermediate flow cell device 762, support material 760 may be arranged within an edge cavity portion 752 between the sidewall 750 of the support frame 734 and the exposed peripheral sides of a plurality of integral, coupled, or unseparated photodetectors 110A, 110B, 110C adjacent to and/or facing it, to couple the support frame 734 and the photodetectors 110A, 110B, 110C together. Since the plurality of photodetectors 110A, 110B, 110C are integral, coupled, or unseparated, the cavity 740 does not extend between adjacent devices 110A, 110B, 110C (therefore, the support material 760 does not extend between adjacent devices 110A, 110B, 110C). As discussed above, multiple different photodetectors 110A, 110B, 110C can be manufactured as part of a wafer of multiple integral or coupled different photodetectors 110A, 110B, 110C. The wafer of the device can be diced into individual different photodetectors (as shown in Figures 10-12B) and/or multiple integral or coupled different photodetectors (including any number of individual different devices) (as shown in Figures 13A and 13B).

Figure 14 illustrates an intermediate flow cell device 862 formed via at least one photodetector 10 within a frame 834 and one or more cavities 840, but without a base substrate or any associated interlayer and/or spacer layer. The intermediate flow cell device 862 of Figure 14 is similar to the intermediate flow cell devices 62 of Figures 11A and 11B, 662 of Figures 12A and 12B, and 762 of Figures 13A and 13B; therefore, similar reference numerals beginning with “8” are used to denote similar components, aspects, functions, processes, or features, and the descriptions relating thereto above also apply, and will not be repeated for the sake of brevity and clarity. Although only a single photodetector 110 is shown in each cavity 840 in Figures 15A and 15B, as discussed above, a cavity 840 may include multiple spaced photodetectors 110, and support material 860 may extend between adjacent spaced photodetectors 110. Furthermore, although the light detection device 10 of FIG1 is shown in each cavity 840, other light detection devices 10, such as the light detection device 110 of FIG2, can also be used as discussed above.

The intermediate flow cell device 862 differs from intermediate flow cell devices 62, 662, and 762 in the structure of the cavity 840 of the support frame 834 and the support material 860. As shown in Figure 14, the cavity 840 extends only partially through the thickness of the support frame 840. The cavity 840 extends from the upper surface 836 to the lower surface 838 of the support frame 840 via a portion of it. Therefore, the bottom portion 841 of the support frame 841 extends between the lower surface 843 of the cavity 840 and the lower surface 838 of the support frame 840, as shown in Figure 14.

As also shown in Figure 14, the bottom layer or bottom portion 863 of the support material 860 can extend above the lower surface 843 of the cavity 840, on which at least one photodetector 10 can be positioned. Thus, the bottom portion 863 of the support material 860 can extend between the lower surface 26 of at least one photodetector 10 and the corresponding lower surface 843 of the cavity 840.

In some examples, a support material 860 may initially be disposed above the lower surface 843 of a cavity 840 to form its bottom portion 863, and at least one photodetector 10 may be placed thereon, such that the bottom portion 863 of the support material 860 is in situ coupled within the corresponding cavity 840 or otherwise holds at least one photodetector 10 for further processing. For example, after at least one photodetector 10 is placed above/on the bottom portion 863 of the support material 860 (e.g., on the lower surface 26 of at least one photodetector 10 positioned on the exposed upper surface of the bottom portion 863 of the support material 860), additional support material 860 may be introduced into the edge cavity portion 852 between the sidewall 850 of the support frame 834 and the outer periphery of at least one photodetector 10 and above the exposed portion of the (pre-formed) bottom portion 863 of the support material 860. In some other examples, the bottom portion 863 of the support material 860 may be absent, and at least one photodetector 10 may be positioned directly on the lower surface 838 of the support frame 840 (or another layer or material may be positioned therebetween).

As shown in Figures 15A and 15B, after the intermediate flow pool device 962 is formed, the upper surface 961 of the support material 960 within the cavity 940 can be exposed. The intermediate flow pool device 962 of Figures 15A and 15B is similar to the intermediate flow pool device 62 of Figures 11A and 11B, the intermediate flow pool device 662 of Figures 12A and 12B, the intermediate flow pool device 762 of Figures 13A and 13B, and the intermediate flow pool device 862 of Figure 14. Therefore, similar reference numerals beginning with "9" are used to indicate similar components, aspects, functions, processes, or features, and the descriptions relating to them above also apply, and will not be repeated for the sake of brevity and clarity. For example, the intermediate flow pool device 962 can be formed by removing or separating the support substrate and any associated interlayers and spacers from the upper surface 936 of the support frame 934, the upper surface 961 of the support material 960, the upper surface 122 of the cross-section 119. Alternatively, if the cavity 840 extends only partially through the support frame 834, the intermediate flow pool device 962 can be formed without a support substrate.

As shown in Figures 15A and 15B, at least a portion of the exposed upper surface 961 of the support material 960 may extend below and between the upper surface/top side 936 of the support frame 931 and the upper portion 122 of at least one adjacent photodetector 110 positioned within the corresponding cavity 940. Although only a single photodetector 110 is shown in Figures 15A and 15B, as discussed above, the cavity 940 may include a plurality of spaced photodetectors 110, and the support material 960 may extend between adjacent spaced photodetectors 110. In such an example, the upper surface 961 of this portion of the support material 960 may extend below and between the upper portions 122 of adjacent photodetectors 110. Thus, the upper surface 961 of the support material 960 positioned throughout the corresponding cavity 940 may include a recessed top side surface portion positioned below the top side 936 of the support frame 931 and below the upper portion 122 of at least one photodetector 110 positioned within the corresponding cavity 940.

In some such intermediate flow cell devices 962, the upper portion 122 of at least one photodetector 110 positioned within a corresponding cavity 940 may not include a reaction structure extending thereon, as shown in FIG15A. As shown in FIG15B, in some such intermediate flow cell devices 962, the reaction structure 120 may be positioned above the upper portion 122 of at least one photodetector 110 and the top side 961 of the support material 960 within the corresponding cavity 940, filling any of its recesses to form a planar upper surface from which a plurality of nanopores 16 extend.

It should be noted that the reaction structure 120 may be positioned above the entire effective area of at least one photodetector 110 on the upper portion 122 of at least one photodetector 110. Therefore, the upper surface of the planar surface of the reaction structure 120 may include the upper surface of the portion of the reaction structure 120 positioned above the support material 960 within the corresponding cavity 940, and the upper surface of the gap region of the reaction structure 120 may be positioned above at least one photodetector 110 within the corresponding cavity 940, and thus may be coplanar.

As also shown in Figure 15B, the reaction structure 120 can further extend above the upper surface 936 of the support frame 934. Therefore, the planar upper surface of the reaction structure 120 can also extend above the upper surface 936 of the support frame 934 surrounding the corresponding cavity 940. Thus, the upper surface of the portion of the reaction structure 120 positioned above the support material 960 within the corresponding cavity 40, the upper surface of the portion of the reaction structure 120 positioned above the upper surface 936 of the support frame 934 surrounding the corresponding cavity 940, and the upper surface of the gap region of the reaction structure 120 positioned above at least one photodetector 110 within the corresponding cavity 940 can be coplanar.

Layer construction methods that can be used to form the reactive structure 120 include photolithography, etching (e.g., reactive ion etching), sputtering, evaporation, casting (e.g., spin coating), chemical vapor deposition, electrodeposition, epitaxial growth, thermal oxidation, physical vapor deposition, etc. In some examples, shading techniques can be used to form the reactive structure 120. In some examples, nanolithography such as nanoimprint lithography (NIL) can be used to form the reactive structure 120. In one example, the reactive structure 120 can be formed at least partially via one or more UV-curable resin layers positioned above the upper surface 936 of the support frame 934, the upper portion 122 of at least one photodetector 110, and the top side 961 of the support material 960 within the corresponding cavity 940 via one or more NIL-related processes.

In one example, the reaction structure 120 may include at least one layer positioned above an upper portion 122 of the photodetector 110, the upper portion 122 being configured as an array of reaction recesses 16 (e.g., nanopores) as discussed above with respect to FIG. 1. In another example, at least one layer of the reaction structure 120 may include a pre-formed reaction recess 16. Optionally, at least one layer of the reaction structure 120 may be etched to remove a portion thereof, forming at least a portion of the reaction recess 16.

In another example, the reaction depressions 16 can be formed by molding at least one layer of the reaction structure 120. For example, NIL material can be disposed at least above the upper portion 122 of the photodetector 110. The NIL material can include materials capable of being imprinted using NIL technology. For example, the NIL material can include polymers. The NIL material can then be imprinted or stamped with a mold (also called a template) having a characteristic pattern for forming the reaction depressions 16 in the NIL layer. In some structures, the mold is transparent, thereby allowing UV or visible light to propagate through it. In such structures, the NIL material can include a photocurable polymer that cures with UV or visible light when the mold is pressed into the NIL. Thus, the NIL material can be cured (e.g., hardened) to form the reaction depressions 16. This method can be the same as or similar to step flash imprinting (SFIL). In other structures, the NIL material can be cured by applying heat and/or pressure.

Figures 16A-16D illustrate an exemplary method of forming a plurality of back-side electrical contacts 1072 on the back side of an intermediate flow cell device 1062, which are capable of transmitting or conducting data signals (based on photons detected by the photosensor 116) from the circuitry 124 of at least one photodetector 110 within a corresponding cavity 1040, so as to transmit the data signals to a biodetector and/or bioassay system when used in a flow cell formed via the intermediate flow cell device 1062. Although the intermediate flow cell device 1062 is shown as having the structure of the intermediate flow cell device 62 of Figures 11A and 11B, the intermediate flow cell device 1062 may have different structures, such as the structure of the intermediate flow cell device 662 of Figures 12A and 12B or the structure of the intermediate flow cell device 762 of Figures 13A and 13B. Therefore, similar reference numerals beginning with "10" are used to denote similar components, aspects, functions, processes, or features, and the descriptions relating to them above also apply, and will not be repeated for the sake of brevity and clarity. It should be noted that the back contact 1072 on the back side of the intermediate flow cell device 1062 is coupled to the back via 128 of at least one photodetector 110 within the corresponding cavity 1040. Therefore, although the intermediate flow cell device 1062 is shown using the photodetector 110 of FIG2, other photodetector structures including the back via 128 can also be used.

As shown in Figures 16A and 16B, a non-conductive substrate or material 1070 is positioned on the back side of the intermediate flow cell device 1062. Also as shown in Figures 16A and 16B, the back side 1074 of the substrate 1070 includes a plurality of exposed conductive back side contacts 1072 coupled thereto. The back side contacts 1072 may be at least partially embedded within the back side 1074 of the substrate 1070. A back side contact 1072 (potentially, independent and distinct back side contacts 1072) may be provided for each back side via 128 (i.e., a uniquely associated via 128) of each photodetector 110 within each cavity 1040. As shown in Figure 16B, adjacent back side contacts 1072 may be spaced apart from each other, and a portion of the substrate 1070 may extend therebetween.

The substrate 1070 may comprise any non-conductive or semiconductor material, such as polymers (e.g., epoxy resin), silicon, glass, ceramics, or combinations thereof. The back contact 1072 may comprise any conductive material, such as a metal (e.g., copper). In some examples, the substrate 1070 and the back contact 1072 may comprise a printed circuit board.

As shown in FIG16B, the substrate 1070 and/or back contact 1072 may include a through-hole 1076, which is at least partially aligned (e.g., overlapped) with the back side 126 of at least one photodetector 110 within each cavity 1040 of the support frame 1034. Therefore, the through-hole 1076 is at least partially aligned (e.g., overlapped) with the opening/space portion between the spacer 130 (if provided) and the via 128, which extends to the substrate portion 114 at the back side 126 of at least one photodetector 110 within each cavity 1040.

As shown in Figure 16C, conductive lines or other structures 1080 may be coupled between vias 128 of at least one photodetector 110 within each cavity 1040 and adjacent or associated back contacts 1072. Lines 1080 may comprise any conductive material, such as metals (e.g., copper). Lines 1080 are capable of transmitting data signals from vias 128 of circuitry 124 of at least one photodetector 110 to the back contacts 1072. Thus, each line 1080 may extend from a corresponding contact 1072 on the back side of the intermediate flow cell device 1062, through an adjacent or associated via 1076, and to a corresponding via 128 of the photodetector 110 within the cavity 1040 of the support frame 1034, as shown in Figure 16C. In some examples, lines 1080 may be spaced inwardly from the inner sidewall of the via 1076.

For a line 1080 coupled between a corresponding via 128 and a back contact 1072, the line 1080 may be covered, sealed/wrapped in an insulating portion 1082, as shown in FIG16D. The insulating portion 1082 may include an electrically insulating material, thereby electrically insulating the line 1080. As shown in FIG16D, the insulating portion 1082 may cover a portion (or all) of the back side 126 of at least one photodetector 110 exposed within each cavity 1040 of the via 1076. For example, the insulating portion 1082 may extend over and fill the space between spacers 130 (if provided) of each photodetector 110 within the corresponding cavity 1040.

Each insulating portion 1082 may also fill the through-hole 1076 and extend only on a portion of the back contact 1072 associated with each cavity 1040 to form an exposed portion of the back contact 1072. For example, the insulating portion 1082 may extend only above (and wrap around) the portion of the back contact 1072 coupled to the corresponding line 1080, such as the portion of the back contact 1072 adjacent to (e.g., adjacent to) the corresponding through-hole 1076. Thus, portions of the back contact 1072 without the insulating portion 1082 (e.g., portions away from the corresponding through-hole 1076) may remain exposed. The exposed portions of the back contact 1072 may be coupled to another structure or device to transmit data signals from at least one photodetector 110. It should be noted that after the insulating portion 1082 is formed, the intermediate flow cell device 1062 may be cut off to form one or more flow cells, as further explained below. For example, a reaction structure may be formed on the photodetector 110 (if it has not already been formed), reaction sites may be formed on the reaction structure of the photodetector 110, and/or the intermediate flow cell device 1062 may be cut off before or after capping.

Figures 17A-17C illustrate another method of forming a plurality of back-side electrical contacts 1172 on the back side of an intermediate flow cell device 1162, which transmit or transfer data signals from circuitry 124 of at least one photodetector 110 (based on photons detected by its photosensor 116) within a corresponding cavity 1140, such as when used to transmit data signals to a biodetector and/or bioassay system for use in a flow cell formed via the intermediate flow cell device 1162. The method of forming the plurality of back-side electrical contacts 1172 and the intermediate flow cell device 1162 of Figures 17A-17C is similar to the method and intermediate flow cell device 1062 of Figures 16A-16D; therefore, similar reference numerals beginning with "11" are used to denote similar components, aspects, functions, processes, or features, and the descriptions relating thereto above also apply, and will not be repeated for the sake of brevity and clarity.

As shown in FIG17A, a conductive back-side contact 1172 is provided on the bottom side 1138 of the support frame 1134. For example, the back-side contact 1172 may be at least partially embedded in the bottom side 1138 of the support frame 1134, as shown in FIG17A. As shown in FIG17A, adjacent back-side contacts 1172 may be spaced apart from each other, and a portion of the support frame 1134 may extend therebetween. In some examples, the back-side contact 1172 may include the bottom portion of the cavity 1140 of the support frame 1134 (i.e., the portion of the sidewall 1150 of the support frame 1134 that forms the cavity 1140). In one example, the back-side contact 1172 and the support frame 1134 may include a printed circuit board. As shown in FIG17B, a line 1190 may be accessible from a corresponding via 128 of the photodetector 110 through its back side 122 to an adjacent (e.g., adjacent) back-side contact 1172. After the wire is coupled to the via 128 and the back contact 1172, the portion of the back side 122 and back contact 1172 of the photodetector 110 coupled to the wire 1180 is covered by an insulating portion 1182, as shown in FIG17C. The wire 1180 is also completely wrapped by the insulating portion 1182. The insulating portion 1182 covers only a portion of the back contact 1172 to leave its exposed portion mating with another structure or device to transmit data signals from at least one photodetector 110. It should be noted that after the insulating portion 1182 is formed, the intermediate flow cell device 1162 may be cut off to form one or more flow cells, as further explained below. For example, the intermediate flow cell device 1162 may be cut off before or after forming a reaction structure on the photodetector 110 (if it has not already been formed), forming reaction sites on the reaction structure of the photodetector 110, and/or capping.

Figures 18A-18C illustrate another method of forming a plurality of back-side electrical contacts 1272 on the back side of an intermediate flow cell device 1262. These back-side electrical contacts 1272 can transmit or conduct data signals from circuitry 124 of at least one photodetector 110 (based on photons detected by its photosensor 116) within a corresponding cavity 1240, such as when used to transmit data signals to a biodetector and/or bioassay system when used in a flow cell formed via the intermediate flow cell device 1262. The method of forming the plurality of back-side electrical contacts 1272 and the intermediate flow cell device 1262 of Figures 18A-18C is similar to the method and intermediate flow cell device 1062 of Figures 16A-16D. Therefore, similar reference numerals beginning with "12" are used to denote similar components, aspects, functions, processes, or features, and the descriptions relating to them above also apply, and will not be repeated for the sake of brevity and clarity.

As shown in Figure 18A, the intermediate flow cell device 1262 may include at least one photodetector 110 within each cavity 1240 without spacers on the back side 126. However, in an alternative example, at least one photodetector 110 within one or more cavities 1240 may include spacers on the back side 126 (as shown in Figure 2). As shown in Figure 18A, vias 128 of the circuitry 124 of the photodetector 110 may be exposed on the back side 126. In one example, as shown in Figure 18A, the exposed end of the via 128 at the back side 126 of the photodetector 110 may be substantially aligned (i.e., coplanar) with the back side 1238 and/or the back side of the support frame 1234.

As shown in Figure 18B, a plurality of conductive interconnects 1278 may be positioned above the back side of the intermediate flow cell device 1262. The interconnects 1278 may comprise any conductive material, such as a metal (e.g., copper), to transmit data signals from the associated photodetector 110. Each interconnect 1278 is electrically coupled to the exposed end surface of a corresponding via 128 at the back side 126 of the photodetector 110 and extends above the back side 1265 of the filler material 1260 within the channel 1252 of the photodetector 110 and a portion of the back side 1238 of the support frame 1234. As shown in Figure 18B, adjacent interconnects 1278 on the back side 1238 of the support frame 1234 may be spaced apart from each other, and a portion of the support frame 1234 may extend therebetween. Similarly, adjacent interconnects 1278 on the back side 126 of the optical detection device 110 may be spaced apart from each other.

Through interconnect contacts 1278 located on the back side 1238 of the support frame 1234, the back side 1265 of the filler material 1260, and the back side 126 of the photodetector 110, a plurality of back side contacts 1272 may be positioned above (e.g., above) a portion of the interconnect contacts 1278, thus electrically coupling them, as shown in FIG18C. In some examples, the back side contacts 1272 may be positioned on the portion of the interconnect contacts 1278 ( wholly or partially) located above the support frame 1234 and/or the filler material 1260, as shown in FIG18C.

As also shown in Figure 18C, the insulating material 1282 may also be positioned above the interconnecting contacts 1278. The insulating material 1282 may extend above the exposed surface area of the interconnecting contacts 1278. The insulating material 1282 may also extend above the back side 126 of the photodetector 110 and above the bottom side 1238 of the support frame 1238 between adjacent interconnecting contacts 1278 and the back contact 1272. Thus, the insulating material 1282 may cover or wrap the back side of the intermediate flow cell device 1262 but not the back contact 1272. Therefore, the exposed portion of the back contact 1272 can be matched with another structure or device to transmit data signals from at least one photodetector 110 to it. It should be noted that after the insulating material 1282 and the back contact 1272 are formed, the intermediate flow cell device 1262 may be cut off to form one or more flow cells, as further explained below. For example, a reaction structure may be formed on the photodetector 110 (if it has not already been formed), reaction sites may be formed on the reaction structure of the photodetector 110, and/or the intermediate flow cell device 1262 may be cut off before or after capping.

Figures 19A-19C illustrate a method for forming a plurality of back-side electrical contacts 1372/1398 on the back side of an intermediate flow cell device 1362, which are capable of transmitting or conducting data signals from circuit 24 of at least one photodetector 10 (based on photons detected by its photosensor 16) within a corresponding cavity 1340, thereby transmitting data signals to a biodetector and/or bioassay system when used for a flow cell formed via the intermediate flow cell device 1362. The method of forming the plurality of back-side electrical contacts 1372 and intermediate flow cell device 1362 of Figures 19A-19C is similar to that of Figures 16A-16D and intermediate flow cell device 1062, Figures 17A-17C and intermediate flow cell device 1162, and Figures 18A-18C and intermediate flow cell device 1262. Therefore, similar reference numerals beginning with "13" are used to indicate similar components, aspects, functions, processes, or features, and the descriptions relating to them above also apply, and will not be repeated for the sake of brevity and clarity. Furthermore, although the photodetector device 10 of Figure 1 is shown in each cavity 1340, other photodetector devices, such as the photodetector device 110 of Figure 2, can also be used as discussed above. It should be noted that photodetector devices that do not extend through their base wafer portion 14 can advantageously be used for the formation of the support frame 1362 and intermediate flow cell device 1362.

As shown in FIG19A, the intermediate flow cell device 1362 includes a support frame 1224 having a plurality of conductive vias 1384 extending from an upper surface 1336 to a lower surface 1338. The vias 1384 may comprise any conductive material, such as a metal (e.g., copper), to transmit data signals from an associated photodetector 110. A portion of the vias 1384 on the bottom side 1338 of the support frame 1334 (i.e., the back side of the intermediate flow cell device 1362) is exposed, forming a back-side electrical contact portion 1372, as shown in FIG19A. Similarly, also as shown in FIG19A, a portion of the vias 1384 on the top side 1336 of the support frame 1334 (i.e., the front side of the intermediate flow cell device 1362) is exposed, forming a front-side electrical contact portion 1373. The back side electrical contact portion 1372 and/or the front side electrical contact portion 1373 may be enlarged (e.g., defining a larger cross-sectional area) compared to the middle portion of the via 1384 extending therebetween.

Adjacent vias 1384 of the support frame 1334 may be spaced apart from each other, and a portion of the support frame 1334 may extend between them. For example, adjacent front-side electrical contact portions 1373 may be spaced apart from each other, and a portion of the support frame 1334 at its top side 1336 may extend therebetween, as shown in FIG19A. Similarly, adjacent back-side electrical contact portions 1372 may be spaced apart from each other, and a portion of the support frame 1334 at its bottom side 1338 may extend therebetween.

As shown in Figure 19B, a plurality of conductive interconnecting contacts 1386 may be positioned on the front side of the intermediate flow cell device 1362 to electrically couple the device circuit 24 of at least one photodetector 10 within each cavity 1340 of the support frame 1334 to the electrical contact portion 1386 of the via 1384 of the support frame 1334. Each interconnecting contact 138 may extend over the portion of the top side 22 of the photodetector 10 containing the exposed portion of the circuit 24, over the portion of the photodetector 10 adjacent to the edge cavity portion 1352 on the top side of the support material 1360, and over the portion of the exposed upper surface of the front electrical contact portion 137 of the via 1384. Thus, the interconnecting contact 138 can electrically couple the circuit 24 of at least one photodetector within the cavity 1340 to the via 1384 extending through the support frame 1334, thereby transmitting (i.e., conducting) data signals from at least one photodetector 10 through it to the back electrical contact portion 1373.

In Figure 19C, the insulating material portion 1382 may be positioned above the interconnecting contact 1386. The insulating material 1382 may extend at least over the exposed surface area of the interconnecting contact 1386. The insulating material 1382 may also extend between adjacent interconnecting contacts 1386 above the top side 1336 of the support frame 1334. Thus, the insulating material 1382 may cover or enclose at least a portion of the conductive components or portions of the intermediate flow cell device 1262 on its top side. The insulating material 1382 may include a substantially planar and/or smooth exposed upper surface 1383, as shown in Figure 19C. For example, the upper surface 1383 of the insulating material 1382 may include/define a submicron-scale surface roughness. In some such examples, the upper surface 1383 of the insulating material 1382 may include/define a surface roughness less than or equal to 50 nm, or less than or equal to 10 nm. In one example, the upper surface 1383 of the insulating material 1382 may include or define a surface roughness in the range of 1-2 nm.

The exposed portion of the back contact 1372 can cooperate with another structure or device to transmit data signals from the respective photodetectors 10. In FIG. 19C, conductive leads or balls 1398 (e.g., partially spherical) may be positioned above (e.g., on) the exposed surface of the back contact portion 1373 of the via 1384 to transmit or conduct signals from at least one photodetector 10 within the cavity 1340 to, for example, a biosensor and/or a bioassay system. The balls 1398 may comprise any conductive material, such as metal solder. Each ball 1398 may extend above the exposed surface of the corresponding back contact portion 1373, above the exposed lower surface of the support material 1360 adjacent to the corresponding back contact portion 1373, and above a portion of the back side 26 associated with the corresponding back contact portion 1373 on the photodetector 10, as shown in FIG. 19C. Sphere 1398 may include intermediate flow pool device 1362 (and one or more flow pools ultimately formed therefrom) of a ball grid arrangement (BGA) type surface mount packaging structure.

At least one flow cell can be formed from the intermediate flow cell device disclosed herein, for example, by forming a reaction structure on a photodetector, forming reaction sites on the reaction structure of the photodetector, capping the photodetector, and/or cutting the intermediate flow cell device. Furthermore, at least one flow cell can be formed via the intermediate flow cell by cutting the intermediate flow cell into one or more discrete cells comprising at least one photodetector, a cap extending above it, and a fluid channel formed between the photodetector and the cap. As described above, for example, the support frame 1334 may include visual indicators to aid in alignment during the capping and/or cutting operations.

In some examples, one or more flow cells may be formed via an intermediate flow cell before forming a back contact electrically coupled to at least one of its photodetectors. For example, at least one flow cell 1302 may be formed by the intermediate flow cell device 1362 of FIG. 19A, the intermediate flow cell device 1062 of FIG. 16A, the intermediate flow cell device 1162 of FIG. 17A, the intermediate flow cell device 1262 of FIG. 18A, or the intermediate flow cell device 1362 of FIG. 19B or 19C. In some other examples, one or more flow cells may be formed via an intermediate flow cell after forming a back contact electrically coupled to at least one of its photodetectors. For example, at least one flow cell 1302 may be formed by the intermediate flow cell device 1062 of FIG. 16D, the intermediate flow cell device 1162 of FIG. 17C, the intermediate flow cell device 1262 of FIG. 18C, or the intermediate flow cell device 1362 of FIG. 19C.

Figure 20 illustrates one or more flow cells 1302 formed by the intermediate flow cell device 1362 of Figure 19C. Although the intermediate flow cell device 1362 of Figure 19B is shown to form one or more flow cells 1302 of Figure 20, the same can also be used, for example, the intermediate flow cell device 1062 of Figure 16A or 16D, the intermediate flow cell device 1162 of Figure 17A or 17C, the intermediate flow cell device 1262 of Figure 18A, 18B or 18C, or the intermediate flow cell device 1362 of Figure 19A or 19B.

As shown in Figure 20, the cover/cover 1396 may extend over the front/top side of the intermediate flow cell device 1362. For example, the lower surface 1397 of the cover 1396 may be attached to an exposed upper surface of the intermediate flow cell device 1362, such as the upper surface 1383 of the insulating material 1382, as shown in Figure 20. In this way, the cover 1396 may extend over the upper portion 20 of at least one photodetector 10 positioned within each cavity 1340, the photodetector 10 including a reaction structure having a detector surface as described above.

As shown in Figure 20, the lower surface 1397 of the cover 1396 may be spaced above the upper portion 22 of at least one photodetector 10 positioned within each cavity 1340, thereby forming a fluid channel 1390 therebetween. Each fluid channel 1390 is configured (e.g., sized and shaped such that it guides fluid, such as a reaction solution, along the detector surface of the reaction structure 20 of the associated at least one photodetector 10. As shown in Figure 20, the sides of the fluid channel 1390 may be defined by an insulating material 1382 and/or a front electrical contact portion 1386. The region of the fluid channel 1390 may be substantially aligned/overlapping with at least one photodetector 10 of each corresponding cavity 1340. For example, the region of the fluid channel 1390 may be substantially aligned and consistent/conform to the effective region of at least one photodetector 10 of each corresponding cavity 1340, as shown in Figure 20. In some other examples, the region of the fluid channel 1390 may be aligned with and extend beyond the effective region of at least one photodetector 10 of each corresponding cavity 1340, as shown in Figure 21. As described above, the support frame 1334 may include visual indicators to help align the position of the cover 1396.

In some examples, the fluid channel 1390 may include a height in the range of about 50-400 μm or about 80-200 μm (extending between the lower surface 1397 of the cover 1396 and the upper portion 22 of at least one photodetector 10, e.g., its detector surface). In one example, the height of the fluid channel 1390 is about 100 μm. The thickness of the cover 1362 may be, for example, about 300 μm to about 1000 μm.

In some other examples, the cover 1396 may be indirectly coupled to the upper surface of at least one photodetector 10, support material 1360, and/or support frame 1334 via an intermediate layer/part different from the insulating material 1382 and/or the front electrical contacts 1386, which may at least partially define or not define the side of the fluid channel 1390. In other examples, the cover 1362 may be directly coupled to the upper surface of at least one photodetector 10, support material 1360, and/or support frame 1334 (e.g., its insulating material or its vias 1384, such as via a low self-fluorescent adhesive). In such an example, the cover 1362 may include a sidewall portion that spaces the lower surface 1397 of the cover 1396 extending above at least one photodetector 10 over the upper portion 22 of at least one photodetector 10. Such a sidewall portion of the cover 1362 may define the side of the fluid channel 1390.

As also shown in Figure 20, the cover 1362 may include at least one port 1362 configured to fluidly engage with the fluid channel 1390 and possibly other ports (not shown). For example, the other ports may originate from a cartridge or workstation containing a reaction solution or another biological or chemical substance. In some examples, the cover 1362 may include at least two ports 1392 associated within each fluid channel 1390 as an inlet and outlet for the fluid channel 1390. In some examples, the diameter of the at least two ports 1392 may be approximately 750 μm. At least one port 1362 allows reagent fluid or solution to flow into and possibly through the associated fluid channel 1390. As explained above, a chemical reaction occurs in the fluid channel 1390 between the reagent solution and the reaction site on the detector surface of the reaction structure 20 on the upper portion 22. When light is emitted through the cover 1362, the photodetector 10 of the flow cell 1302 is able to sense the chemical reaction occurring in the fluid channel 1390 and generate a signal in response to that reaction. As explained above, the signal can be transmitted via circuitry 24 of the photodetector 10 to the back contact 1372 (and ball contact 1398, if provided). Therefore, the cover 1362 may comprise a material transparent to excitation light propagating from outside the flow cell 1302 into/from the fluid channel 1390. It should be noted that the excitation light can approach the cover 1362 at any angle and at the same or different angles. In some examples, the cover 1362 may comprise a material that is at least optically transparent to the excitation light and has low or no autofluorescence, such as, but not limited to, cyclic olefin copolymers (COCs).

As shown in Figure 20, the reaction structure 20 may be positioned on the upper portion 22 of each photodetector 10 before or after the cap 1362 is attached to the intermediate flow cell device 1362. As further explained above and below, the detector surface of the reaction structure 20 on the upper portion 22 of each photodetector 10 may extend over the entire effective area of each corresponding photodetector 10. As discussed above, the detector surface of the reaction structure 20 may include nanopores 16 extending into the reaction structure 20 and planar gap surfaces extending between and around the nanopores 16.

The detector surface of each photodetector 10 can be functionalized (e.g., chemically or physically modified in a manner suitable for carrying out a specified reaction). For example, the detector surface can be functionalized and can include at least one reaction site located on/within a nanopore 16 on which one or more molecules are immobilized. The reaction site can include a biological or chemical substance configured to initiate a reaction and/or form a reaction product that generates or emits a light signal in response to excitation light. In a particular example, the reaction site can include clusters or colonies of biomolecules (e.g., oligonucleotides) immobilized on the detector surface within the nanopore 16. For example, after treatment with a reaction solution, the reaction site can generate light emission in response to incident excitation light. Excitation light can be emitted or generated from any light-emitting system or source (not shown), which may or may not be part of the flow cell 1302. In some examples, the light-emitting system can emit excitation light of a specific wavelength or a specific number of wavelengths that excites the biological or chemical substance at the reaction site (e.g., a reaction initiated by a reaction solution and/or a reaction product formed by the reaction solution at the reaction site 114).

Initially, the reaction sites of the nanopores 16 of the reaction structure 20 of the photodetector 10 may not include a designated reaction. As discussed above, the reaction sites may include biological or chemical substances attached to the detector surface on the lower and/or side surfaces of the nanopores 16. In a particular example, the reaction sites are located near the opening of at least one corresponding photosensor 18, such that after a designated reaction occurs by treatment with a reaction solution, the emission of designated or predetermined light from the reaction sites propagates through the reaction structure 20, through at least one corresponding photosensor 18, and to at least one corresponding photosensor 12.

The biological or chemical substance at a single reaction site can be similar or identical (e.g., a colony of an analyte (e.g., an oligonucleotide) with a shared sequence). However, in other examples, a single reaction site and/or nanopore 16 may comprise a different biological or chemical substance. Prior to the specified reaction, the reaction site may comprise at least one analyte (e.g., a target analyte). For example, the analyte may be an oligonucleotide or a colony thereof (e.g., a target oligonucleotide). The oligonucleotide may have a valid shared sequence and bind to a predetermined or specific fluorescently labeled biomolecule (e.g., a fluorescently labeled nucleotide).

However, prior to the designated reaction, the fluorophore of the fluorescently labeled biomolecule is not added to or bound to the biological or chemical substance (e.g., oligonucleotide) at reaction site 114. To achieve the designated reaction (i.e., adding the fluorescently labeled biomolecule to the biological or chemical substance at reaction site 114), flow cell 1303 may provide a flow of reaction solution into fluid channel 1390, thereby entering reaction structure 20. The reaction solution can be any solution. In some examples, the reaction solution may include a liquid. For example, the reaction solution may be an aqueous solution. In one embodiment, the reaction solution contains one or more nucleotides, at least some of which are fluorescently labeled, and the reaction solution also contains one or more biomolecules, such as polymerases, which add nucleotides to the growing oligonucleotide at the reaction site, thereby labeling the oligonucleotide with the fluorescently labeled nucleotide. In this embodiment, flow cell 1302 may provide a washing solution to remove any free nucleotides not added to the oligonucleotide. The reaction site may then be irradiated with excitation light, initiating fluorescence in those reaction sites where fluorescently labeled nucleotides have been added. Reaction sites where no fluorescently labeled nucleotides have been added do not emit light under incident excitation light.

As shown in Figures 20 and 21, since the cover 1390 is (directly or indirectly) connected to the area of the support frame 1334 and/or support material 1360 associated with each cavity 1340, the area of each fluid channel 1390 is configured to extend entirely above the detector surface of the reaction structure 20, such that each fluid channel 1390 spans the entire (e.g., at least 95% or at least 99% or 100%) effective area 1306 of at least one photodetector 10 in the corresponding cavity 1340. Because the fluid channel 1390 is aligned with or extends through the effective area 1306 of at least one photodetector 10 in each or multiple corresponding cavities 1340, the flow cell 1302 may include approximately 100% of the effective area 1306 of at least one photodetector 10 within each corresponding cavity 1340 for reagent delivery and luminescence. In one example, the mold size of the photodetector 10 corresponding to cavity 1340 can be approximately 8 mm x 9 mm, and its effective area 1306 can be approximately 7 mm x 8 mm. However, the mold size and/or effective area 1306 of the photodetector 10 can be, for example, up to approximately 25 mm x 25 mm. As described above, each fluid channel 1390 can be aligned with or extend through the effective area 1306 of at least one photodetector 10 in each or multiple cavities 1340 (and at least one photodetector 10 itself). Therefore, the area of the fluid channel 1390 can be larger than the effective area 1306 of at least one photodetector 10 in each or multiple cavities 1340.

Multiple flow cells 1302 can be formed from the intermediate flow cell device disclosed herein. For example, Figures 20 and 22 illustrate the formation of one or more discrete flow cells 1302, which can be formed from the intermediate flow cell device 1362. As shown in Figure 20, the intermediate flow cell device 1362 can be cut at the cutting line 1304 to divide it into one or more independent and distinct flow cells as individual portions of the intermediate flow cell device 1362. It should be noted that the intermediate flow cell device 1362 can be cut off after or before the cap 1396 is coupled to it. Similarly, the surface of the intermediate flow cell device 1362 can be cut off after or before the formation of its reaction structure 20 and/or reaction sites on/in the nanopores 16 on the upper surface of the photodetector 10. As another example, the intermediate flow cell device 1362 can be cut off after or before the formation of the back-side electrical contacts (such as ball contacts 1398) of the flow cell. As described above, the support frame 1334 may include visual indicators to help align the intermediate flow pool device 1362 during the cutting process.

As shown in Figure 22, the intermediate flow cell device 1362 can be cut to form multiple independent and different flow cells 1302A, 1302B, 1302C. It should be noted that although three flow cells 1302A, 1302B, 1302C are used herein to illustrate the formation of flow cells from the intermediate flow cell device, any number of flow cells can be used (e.g., one flow cell, two flow cells, three flow cells, four flow cells, five flow cells, etc.). Cutting the flow cells 1302A, 1302B, 1302C may include the same number and/or structure of photodetector devices 10/cavities 1340, or may include different numbers and/or structures of photodetector devices 10/cavities 1340. For example, a first cut flow pool 1302A formed from the intermediate flow pool device 1362 may include a single cavity 1340 (fluid channels 1390 positioned over its entire (e.g., at least 95% or at least 99% or 100%) effective area), the single cavity 1340 including a first structure (e.g., light detection device 10 and/or light detection device 110) and a first number of light detection devices (e.g., one or more light detection devices), as shown in FIG22. A second cut flow pool 1302B may also be formed from the intermediate flow pool device 1362, which includes a pair of cavities 1340 (fluid channels 1390 positioned over its entire (e.g., at least 95% or at least 99% or 100%) effective area), the cavity 1340 including a second structure (e.g., light detection device 10 and/or light detection device 110) and a second number of light detection devices (e.g., one or more light detection devices). The second number and/or second structure of the photodetectors in the second cutting flow cell 1302B may be the same as or different from that in the first cutting flow cell 1302A. Similarly, as shown in FIG22, a third cutting flow cell 1302C may also be formed by the intermediate flow cell device 1362, which may include three or more cavities 1340 (fluid channels 1390 are positioned over their entire (e.g., at least 95% or at least 99% or 100%) effective area), each cavity 1340 including a third number of photodetectors (e.g., one or more photodetectors) with a third structure (e.g., photodetector 10 and/or photodetector 110). The third number and/or third structure of the photodetectors in the third cutting flow cell 1302C may be the same as or different from that in the first cutting flow cell 1302A and the second cutting flow cell 1302B. Thus, the sensing throughput of different flow cells 1302A, 1302B, 1302C formed by the intermediate flow cell device 1462 (which is cut from the intermediate flow cell device 1362 to form different flow cells 1302A, 1302B, 1302C) can be determined or set by the number and/or structure of the cavities 1340 (and the number and/or structure of at least one optical detection device 10 therefrom).

It should be understood that the above description is exemplary only and not restrictive. For example, the above examples (and/or aspects thereof) may be used in combination with each other. Furthermore, many modifications may be made to adapt a particular situation or material to the teachings of the various examples without departing from their scope. Although the dimensions and types of materials are described herein, they are intended to define some parameters in the various examples, but they are by no means limiting to all examples and are merely illustrative. Many other examples will be apparent to those skilled in the art upon reading the above description. Therefore, the scope of the various examples should be determined by reference to the appended claims and the full scope of equivalents enjoyed by such claims.

In the appended claims, the terms “including” and “in which” are used as concise English equivalents to the corresponding terms “comprising” and “wherein”. Furthermore, in the following claims, the terms “first,” “second,” and “third” are used only as reference marks and are not intended to impose quantity, structure, or other requirements on their objectives. The term “based on” in this document includes relationships where an element is partially based and relationships where an element is completely based. The term “defined” in this document includes relationships where an element is partially defined and relationships where an element is completely defined. Furthermore, the limitations of the following claims are not written in the form of means plus function, nor are they intended to be interpreted based on paragraph 6 of 35 U.S.C. § 112, unless and until such a claim limitation expressly uses the term “means for…” before a statement of a functional cavity for further construction. It should be understood that not all of the foregoing objects or advantages can be achieved according to any particular example. Therefore, for example, those skilled in the art will recognize that the means, systems, and methods described herein can be implemented or carried out in a manner that achieves or optimizes one or more advantages taught herein, without necessarily achieving other objects or advantages taught or suggested herein.

Although the invention has been described in detail with reference to only a limited number of examples, it should be readily understood that the invention is not limited to such disclosed examples. Rather, modifications can be made to the invention to incorporate any number of variations, alterations, substitutions, or equivalent arrangements not described above but commensurate with the spirit and scope of the invention. Furthermore, although various examples have been described, it should be understood that aspects of the invention may include only one example or some of the examples described. Similarly, although some disclosures are described as having a certain number of elements, it should be understood that the examples may be implemented with fewer or more than that number of elements.

It should be understood that all combinations of the foregoing concepts and the additional concepts discussed in more detail below (assuming that such concepts do not contradict each other) are considered part of the inventive subject matter disclosed herein. In particular, all combinations of the claimed subject matter appearing at the end of this invention are considered part of the inventive subject matter disclosed herein.

Claims (20)

1. A flow cell, comprising: a) A support frame including a top side, a bottom side, and at least one cavity extending from the top side to the bottom side, wherein the support frame further includes at least one conductive via extending from the top side to the bottom side. b) At least one optical detection device disposed within the at least one cavity, wherein the at least one optical detection device comprises: i) the upper surface; and ii) At least one solid-state photodetector comprising a base wafer portion forming a back side, a plurality of photosensors, a plurality of photoconductors associated with the plurality of photosensors, and device circuitry electrically coupled to the plurality of photosensors to transmit photon data signals detected by the plurality of photosensors. The device circuitry further includes vias extending through the base wafer portion, and The at least one optical detection device is electrically coupled to at least one conductive via on the top side of the support frame; c) A support material disposed in at least one cavity between the periphery of the support frame and the at least one photodetector, thereby coupling the support frame and the at least one photodetector together; d) A cover that extends from the at least one light detection device and is coupled to the top side of the support frame around the periphery of the at least one light detection device. A fluid channel is formed between the cover and at least the upper surface of the at least one optical detection device; e) An electrical contact, which is at least partially disposed along the bottom side of the support frame and electrically coupled to at least one conductive via in the support frame. 2. The flow cell of claim 1, wherein the at least one photodetector further comprises a reaction structure disposed above a plurality of photoguides forming the upper surface of the at least one photodetector. 3. The flow cell of claim 2, wherein the reaction structure comprises a plurality of nanopores located within an effective region on the upper surface of the at least one photodetector. 4. The flow tank of claim 1, wherein the cover is indirectly coupled to the top side of the support frame. 5. The flow cell of claim 1, wherein the at least one photodetector comprises a plurality of photodetectors disposed within the at least one cavity. 6. The flow cell of claim 5, wherein the plurality of photodetectors comprises different photodetectors spaced apart from each other, and wherein the support material further extends between adjacent photodetectors. 7. The flow cell of claim 6, wherein the plurality of photodetectors comprises at least two integrated photodetectors. 8. The flow cell of claim 1, wherein the at least one photodetector comprises a plurality of photodetectors, wherein the at least one cavity comprises a plurality of cavities, and wherein each of the plurality of photodetectors is disposed in a different cavity of the plurality of cavities. 9. The flow cell of claim 1, wherein the at least one cavity extends from the top side through the support frame to the bottom side. 10. The flow cell of claim 1, wherein the at least one cavity extends only partially from the top side to the bottom side through the support frame. 11. The flow cell of claim 1, wherein the at least one photodetector comprises at least one complementary metal-oxide-semiconductor (CMOS) photosensor. 12. The flow cell of claim 1, wherein the flow channel extends over the entire effective area of the at least one photodetector. 13. Methods, including: a) Attaching the upper surface of the support frame to the planar support surface of the substrate, the support frame comprising: i. at least one cavity extending from its top side to its bottom side, and ii. At least one conductive via extending from the top side to the bottom side; b) Positioning at least one photodetector within the at least one cavity, with its top side positioned on the planar support surface of the substrate, and an edge portion of the cavity extending between the support frame and the outer periphery of the at least one photodetector, the at least one photodetector including an effective region and a top surface, wherein the at least one photodetector comprises at least one solid-state photodetector, the at least one photodetector including a base wafer portion forming a back side, a plurality of photosensors, a plurality of photoconductors associated with the plurality of photosensors, and device circuitry electrically coupled to the plurality of photosensors to transmit photon data signals detected by the plurality of photosensors. The device circuitry includes vias extending through the base wafer portion to its back side. The device is electrically coupled to at least one conductive via on the top side of the support frame. c) Fill the edge portion of the cavity with a support material to couple the support frame and the at least one photodetector together; d) Separate the support frame and the substrate; e) Attach a cover to the top side of the support frame around the outer periphery of the at least one optical detection device to form a flow pool, the cover extending above the at least one optical detection device and forming a fluid channel between the cover and at least the upper surface of the at least one optical detection device; f) Electrically couple the device circuitry of the at least one solid-state optical detection device to at least one conductive via on the top side of the support frame; and g) Electrically couple contacts, at least partially along the bottom side of the support frame, to vias on the back side of the base wafer portion. 14. The method of claim 13, further comprising forming a reactive structure on the at least one photodetector prior to attaching the cap, the reactive structure forming an upper surface of the at least one photodetector and including a plurality of nanopores located within the effective region. 15. The method of claim 14, wherein separating the support frame and the substrate exposes a recessed top side of the support material, the support material extending below the top side of the support frame and between the top side of the support frame and the top of the at least one photodetector, wherein the reactive structure extends on the recessed top side of the support material and the top side of the support frame, and wherein the reactive structure forms an upper surface of a plane from which the plurality of nanopores extend. 16. The method of claim 13, further comprising obtaining the at least one optical detection device, wherein the at least one optical detection device comprises cutting at least one complementary metal-oxide-semiconductor (CMOS) optical sensor from a plurality of integrated CMOS optical sensors. 17. The method of claim 13, wherein the fluid channel extends over the entire effective area of the at least one optical detection device. 18. A method for manufacturing a flow cell according to claim 1, comprising: A first support material is disposed on the bottom portion of at least one cavity of the support frame, the at least one cavity extending only partially through the support frame from its top side to its bottom side; At least one optical detection device is positioned within the at least one cavity and on the provided first support material, such that the edge portion of the at least one cavity extends between the support frame and the outer periphery of the at least one optical detection device, the at least one optical detection device including an effective area and an upper surface; The edge portion of the cavity is filled with a second support material; and A cover is attached to the top side of the support frame around the periphery of the at least one optical detection device to form a flow pool, the cover extending above the at least one optical detection device and forming a fluid channel between the cover and at least the upper surface of the at least one optical detection device. 19. The method of claim 18, wherein the fluid channel extends over the entire effective area of the at least one optical detection device. 20. The method of claim 18, further comprising cutting the support frame.