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WO2024138630A1 - Procédé et appareil de codage de données géniques, procédé et appareil de décodage de données géniques, et système de test génétique - Google Patents

Procédé et appareil de codage de données géniques, procédé et appareil de décodage de données géniques, et système de test génétique Download PDF

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Publication number
WO2024138630A1
WO2024138630A1 PCT/CN2022/143914 CN2022143914W WO2024138630A1 WO 2024138630 A1 WO2024138630 A1 WO 2024138630A1 CN 2022143914 W CN2022143914 W CN 2022143914W WO 2024138630 A1 WO2024138630 A1 WO 2024138630A1
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Prior art keywords
signal
gene
carrier
excitation light
identifier
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PCT/CN2022/143914
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English (en)
Chinese (zh)
Inventor
张海洲
彭乐立
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MGI Tech Co Ltd
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MGI Tech Co Ltd
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Priority to PCT/CN2022/143914 priority Critical patent/WO2024138630A1/fr
Priority to CN202280102798.3A priority patent/CN120418452A/zh
Publication of WO2024138630A1 publication Critical patent/WO2024138630A1/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
    • C12M1/00—Apparatus for enzymology or microbiology
    • C12M1/34—Measuring or testing with condition measuring or sensing means, e.g. colony counters
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00—Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63—Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64—Fluorescence; Phosphorescence

Definitions

  • the DVD sequencer will use an optical drive and a laser reader as a chip carrier and signal acquisition device, using the laser light source in the laser reader to excite the fluorescence signal, and the photodetector in the reader to acquire the signal, and then use the optical drive algorithm to process the acquired fluorescence signal.
  • ADC A/D converter
  • the 55 rule must be followed, that is, the oscilloscope sampling rate is more than 5 times the bandwidth, and the bandwidth is more than 5 times the frequency of the measured signal.
  • the method for encoding the gene data further comprises:
  • the fluorescence signal and the reflected light signal are converted into voltage signals respectively.
  • the first signal threshold and the second signal threshold are the same voltage threshold.
  • the optical feature includes the second optical feature and the first optical feature sequentially arranged along a collection path.
  • the excitation light irradiates the gene carrier, comprising:
  • the first excitation light and the second excitation light are alternately used to irradiate the gene carrier.
  • the fluorescence signal includes a first fluorescence signal generated by the first excitation light and a second fluorescence signal generated by the second excitation light
  • the first identifier includes a first sub-identifier corresponding to the first fluorescence signal and a second sub-identifier corresponding to the second fluorescence signal
  • the reflected light signal includes a first reflected light signal corresponding to the first excitation light and a second reflected light signal corresponding to the second excitation light, and the first reflected light signal and the second reflected light signal correspond to the same second identifier;
  • the carrier spots on the gene carrier are distributed in concentric circles along the center of the gene carrier.
  • the loading spots on the gene carrier are distributed in a spiral shape from the center of the gene carrier.
  • the present application provides a method for decoding gene data on a gene carrier, the decoding method comprising:
  • the gene sequence corresponding to the coding sequence is identified.
  • the present application provides a device for encoding genetic data on a gene carrier, wherein a plurality of carriers are provided on the gene carrier, wherein the carriers support samples to be detected having a genetic sequence, and at least one associated position of each of the carriers has an optical feature, and the encoding device comprises:
  • An excitation light source is used to illuminate the gene carrier, excite the sample to be detected to generate a fluorescent signal, and generate a reflected light signal at at least one associated position of each carrier point;
  • a collector for collecting the fluorescence signal and the reflected light signal
  • a comparator connected to the collector, compares the fluorescence signal with a first signal threshold and generates a first identifier according to the comparison result, and compares the reflected light signal with a second signal threshold and generates a second identifier according to the comparison result;
  • An encoder generates a coding sequence associated with the gene sequence based on the first identifier and the second identifier.
  • the optical feature includes a first optical feature that reflects the excitation light and/or a second optical feature that absorbs the excitation light.
  • the first signal threshold and the second signal threshold are both voltage thresholds
  • the gene data encoding device also includes:
  • a converter converts the fluorescence signal and the reflected light signal into voltage signals respectively.
  • the first signal threshold and the second signal threshold are the same voltage threshold.
  • the optical feature includes the second optical feature and the first optical feature sequentially arranged along a collection path.
  • the excitation light includes a first excitation light of a first wavelength and a second excitation light of a second wavelength;
  • the excitation light source alternately uses the first excitation light and the second excitation light to irradiate the gene carrier.
  • the fluorescent signal includes a first fluorescent signal generated by the first excitation light and a second fluorescent signal generated by the second excitation light
  • the first identifier includes a first sub-identifier corresponding to the first fluorescent signal and a second sub-identifier corresponding to the second fluorescent signal
  • the reflected light signal includes a first reflected light signal corresponding to the first excitation light and a second reflected light signal corresponding to the second excitation light, and the first reflected light signal and the second reflected light signal correspond to the same second identifier;
  • the coding sequence includes a first coding sequence formed by combining the first sub-identifier and the second identifier, and a second coding sequence formed by combining the second sub-identifier and the second identifier.
  • the carrier spots on the gene carrier are distributed in concentric circles along the center of the gene carrier.
  • the loading spots on the gene carrier are distributed in a spiral shape from the center of the gene carrier.
  • the present application provides a genetic data decoding device for genetic data on a genetic carrier, wherein a plurality of carriers are arranged on the genetic carrier, the carriers support samples to be detected having a genetic sequence, and at least one associated position of each of the carriers has an optical feature;
  • the decoding device identifies a gene sequence corresponding to the coding sequence.
  • the present application provides a gene detection system, comprising a gene carrier, an excitation light source, and an optical reading device corresponding to the gene carrier, wherein a plurality of carriers are arranged on the gene carrier, the carriers support samples to be detected having gene sequences, and at least one associated position of each of the carriers has an optical feature;
  • the excitation light source illuminates the gene carrier, excites the sample to be detected to generate a fluorescent signal, and generates a reflected light signal at at least one associated position of each carrier point,
  • the optical reading device comprises:
  • a photoelectric detector moves relative to the gene carrier to acquire the fluorescence signal and the reflected light signal
  • the excitation light source includes a first excitation light source for exciting the first fluorescent signal, and a second excitation light source for exciting the second fluorescent signal, and a wavelength of the first excitation light source is different from a wavelength of the second excitation light source.
  • the at least one associated position reacts consistently to the excitation light of the light source.
  • FIG. 6 is a module diagram of a genetic data decoding device according to an embodiment of the present application.
  • FIG. 9 is a flow chart of gene data signal collection of a gene detection system according to an embodiment of the present application.
  • the encoding method of gene data in this embodiment includes:
  • the associated position of the loading point can be various areas adjacent to the loading point centered on the loading point, such as the front area, rear area, or left and right areas of the loading point, and this embodiment does not specifically limit this.
  • the first signal threshold and the second signal threshold can be a voltage threshold Vth
  • the first signal threshold and the second signal threshold can be the same voltage threshold, or can be different voltage thresholds
  • the voltage threshold can be 1V, 2V, 3.3V or 5V, etc., which is not particularly limited in this embodiment.
  • the gene data encoding device of this embodiment further includes:
  • the typical characters A, G, C, and T in the gene sequence can be encoded using a preset encoding method, and A, G, C, and T correspond to adenine, guanine, cytosine, and thymine in DNA, respectively.
  • A can be represented by 00
  • G can be represented by 01
  • C can be represented by 10
  • T can be represented by 11.
  • the excitation light source 11 alternately uses the first excitation light and the second excitation light to irradiate the gene carrier.
  • the first coding sequence corresponding to the first detection path is formed by combining the first sub-identifier and the second identifier
  • the second coding sequence corresponding to the second detection path is formed by combining the second sub-identifier and the second identifier.
  • the biochip is subjected to a similar special process and the biological information is subjected to specific coding processing, for example, a sample to be tested of a gene sequence supported by a carrier point corresponds to multiple DNBs, thereby further improving data utilization.
  • This embodiment improves the continuity, storage efficiency and density of genetic data encoding by performing specific process processing on the biochip and combining the base signals at the corresponding positions for biological encoding.
  • the error rate of genetic data synthesis and data recovery is reduced, and the complexity of signal acquisition and processing is reduced and the processing speed is improved, which meets the requirements of fast, efficient and low-cost detection of genetic sequencers.
  • This embodiment also provides a decoding device for gene data on a gene carrier.
  • a plurality of carrier points are arranged on the gene carrier.
  • the carrier points support samples to be detected having gene sequences. At least one associated position of each carrier point has an optical feature.
  • the acquisition device may be a photodetector.
  • the decoding device identifies the gene sequence corresponding to the coding sequence. Preferably, the decoding device identifies the corresponding gene sequence based on the above-mentioned preset coding conversion table.
  • the optical feature includes a first optical feature that reflects the excitation light and/or a second optical feature that absorbs the excitation light.
  • the excitation light source 32 illuminates the gene carrier 31, excites the sample to be detected to generate a fluorescent signal, and generates a reflected light signal at at least one associated position of each carrier point 311.
  • the optical reading device 33 comprises:
  • the photoelectric detector 331 moves relative to the gene carrier 31 to obtain the fluorescence signal and the reflected light signal.
  • the decoder 333 connected to the encoder 332 identifies the gene sequence corresponding to the coding sequence.
  • the gene sequence is identified based on the above-mentioned preset coding conversion table.
  • the optical reading device 33 is rotatably disposed relative to the gene carrier 31 .
  • the optical reading device 33 and the gene carrier 31 can be relatively rotated, and the decoder 333 can identify the gene sequence corresponding to the coding sequence according to the preset encoding conversion table, thereby completing the encoding and decoding process.
  • the fluorescent signal includes a first fluorescent signal and a second fluorescent signal
  • the optical reading device includes a first detection channel for identifying and acquiring the first fluorescent signal, and a second detection channel for identifying and acquiring the second fluorescent signal.
  • the excitation light source 31 includes a first excitation light source for exciting a first fluorescent signal and a second excitation light source for exciting a second fluorescent signal.
  • the wavelength of the first excitation light source is different from that of the second excitation light source.
  • a multi-channel encoding or decoding system can be formed, thereby meeting the multi-channel sequencing requirements of existing sequencers without excessive signal processing.
  • FIG8 shows the existing gene data signal collection process
  • FIG9 is the gene data signal collection process of the gene detection system of this embodiment. Comparing FIG8 and FIG9, the early signal of this embodiment will be processed by a pure analog circuit to complete photoelectric sampling, I ⁇ V conversion amplification, signal calibration, signal analysis, etc. After the APD signal is amplified by I ⁇ V conversion, it is converted again by a comparator to output high and low levels to distinguish the presence or absence of biological information.
  • the gene detection system of this embodiment collects base signals through a pure analog circuit, which reduces the sampling difficulty and avoids the problem that in the photoelectric sampling stage of the existing gene detection system (gene sequencer), the current value is positively correlated with time and light intensity, and its photosensitivity time is inversely proportional to the linear speed.
  • the chip linear speed is uneven, the signal amplitude and period are unstable, which leads to problems such as difficult signal analysis.
  • the gene detection system of this embodiment uses biochip (gene carrier) for encoding and hardware decoding. It reduces the complexity of signal acquisition and processing, improves the processing speed, and has high data utilization, saving storage space. At the same time, since the image capture no longer requires a camera, a photoelectric detector is used to convert the optical signal into an electrical signal, which reduces the cost and better meets the requirements of fast, efficient and low-cost detection of gene sequencers.
  • biochip gene carrier

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Abstract

Procédé et appareil de codage des données géniques, procédé et appareil de décodage des données géniques et système de test génétique. Une pluralité de points d'appui sont présents sur une lame génique, et les points de portage soutiennent un échantillon à détecter présentant une séquence génique. Le procédé de codage comprend : l'irradiation d'une lame de gène avec une lumière d'excitation, l'excitation d'un échantillon à détecter de manière à générer un signal de fluorescence, et la génération d'un signal de lumière réfléchie à au moins une position associée de chaque point de portage ; l'acquisition du signal de fluorescence et du signal de lumière réfléchie, la comparaison du signal de fluorescence avec un premier seuil de signal et l'exécution d'un codage en fonction d'un résultat de comparaison pour générer un premier identifiant, et la comparaison du signal de lumière réfléchie avec un deuxième seuil de signal et la génération d'un deuxième identifiant en fonction d'un résultat de comparaison ; et sur la base du premier identifiant et du deuxième identifiant, la génération d'une séquence de codage associée à une séquence génique. Dans le procédé, un traitement de signal redondant n'est pas nécessaire, ce qui permet d'éviter la charge de travail importante du traitement de données provoquée par l'acquisition de CAN classique, de rendre la quantité totale de données petite, d'économiser l'espace de stockage, d'augmenter le taux d'utilisation de données, et de réduire le coût.
PCT/CN2022/143914 2022-12-30 2022-12-30 Procédé et appareil de codage de données géniques, procédé et appareil de décodage de données géniques, et système de test génétique Ceased WO2024138630A1 (fr)

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Application Number Priority Date Filing Date Title
PCT/CN2022/143914 WO2024138630A1 (fr) 2022-12-30 2022-12-30 Procédé et appareil de codage de données géniques, procédé et appareil de décodage de données géniques, et système de test génétique
CN202280102798.3A CN120418452A (zh) 2022-12-30 2022-12-30 基因数据的编码和解码方法、装置及基因检测系统

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PCT/CN2022/143914 WO2024138630A1 (fr) 2022-12-30 2022-12-30 Procédé et appareil de codage de données géniques, procédé et appareil de décodage de données géniques, et système de test génétique

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Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000047996A2 (fr) * 1999-02-09 2000-08-17 Illumina, Inc. Traitement informatise d'informations dans des groupements ordonnes de maniere aleatoire
JP2005091125A (ja) * 2003-09-17 2005-04-07 Sony Corp 基板、検査システム、検査装置および方法、記録媒体、プログラム、データ記憶媒体、並びにデータ構造
WO2015158911A1 (fr) * 2014-04-17 2015-10-22 AyoxxA Biosystems GmbH Dispositif codé et procédé de codage et de décodage de zones de référence sur un substrat
CN111710687A (zh) * 2014-08-08 2020-09-25 宽腾矽公司 基于入射光子到达时间的识别、成像、测序法及存储介质
CN111926065A (zh) * 2020-09-18 2020-11-13 中国科学院上海高等研究院 一种高效的核酸检测和基因测序方法及其装置
WO2022094803A1 (fr) * 2020-11-04 2022-05-12 深圳华大智造科技股份有限公司 Système de test
WO2022217112A1 (fr) * 2021-04-09 2022-10-13 Ultima Genomics, Inc. Systèmes et procédés de criblage spatial d'analytes
CN115380203A (zh) * 2020-02-12 2022-11-22 深圳华大智造科技股份有限公司 光学成像系统及应用所述光学成像系统的生化物质检测系统

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000047996A2 (fr) * 1999-02-09 2000-08-17 Illumina, Inc. Traitement informatise d'informations dans des groupements ordonnes de maniere aleatoire
JP2005091125A (ja) * 2003-09-17 2005-04-07 Sony Corp 基板、検査システム、検査装置および方法、記録媒体、プログラム、データ記憶媒体、並びにデータ構造
WO2015158911A1 (fr) * 2014-04-17 2015-10-22 AyoxxA Biosystems GmbH Dispositif codé et procédé de codage et de décodage de zones de référence sur un substrat
CN111710687A (zh) * 2014-08-08 2020-09-25 宽腾矽公司 基于入射光子到达时间的识别、成像、测序法及存储介质
CN115380203A (zh) * 2020-02-12 2022-11-22 深圳华大智造科技股份有限公司 光学成像系统及应用所述光学成像系统的生化物质检测系统
CN111926065A (zh) * 2020-09-18 2020-11-13 中国科学院上海高等研究院 一种高效的核酸检测和基因测序方法及其装置
WO2022094803A1 (fr) * 2020-11-04 2022-05-12 深圳华大智造科技股份有限公司 Système de test
WO2022217112A1 (fr) * 2021-04-09 2022-10-13 Ultima Genomics, Inc. Systèmes et procédés de criblage spatial d'analytes

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