BR112018074572B1 - Métodos de identificação de nucleotídeos e para calibrar um instrumento de sequenciamento, meio de armazenamento legível em computador não transitório, dispositivo e instrumento de sequenciamento - Google Patents

Métodos de identificação de nucleotídeos e para calibrar um instrumento de sequenciamento, meio de armazenamento legível em computador não transitório, dispositivo e instrumento de sequenciamento Download PDF

Info

Publication number
BR112018074572B1
BR112018074572B1 BR112018074572-3A BR112018074572A BR112018074572B1 BR 112018074572 B1 BR112018074572 B1 BR 112018074572B1 BR 112018074572 A BR112018074572 A BR 112018074572A BR 112018074572 B1 BR112018074572 B1 BR 112018074572B1
Authority
BR
Brazil
Prior art keywords
light
nucleotide incorporation
characteristic
points
fact
Prior art date
Application number
BR112018074572-3A
Other languages
English (en)
Portuguese (pt)
Other versions
BR112018074572A2 (pt
Inventor
Jonathan M. Rothberg
Craig Wenger
Mel Davey
Keith G. Fife
Jimmy Jia
Brian Reed
Brett J. Gyarfas
Original Assignee
Quantum-Si Incorporated
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Quantum-Si Incorporated filed Critical Quantum-Si Incorporated
Publication of BR112018074572A2 publication Critical patent/BR112018074572A2/pt
Publication of BR112018074572B1 publication Critical patent/BR112018074572B1/pt

Links

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10Sequence alignment; Homology search
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64Fluorescence; Phosphorescence
    • G01N21/6428Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B45/00ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64Fluorescence; Phosphorescence
    • G01N21/6428Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G01N2021/6439Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" with indicators, stains, dyes, tags, labels, marks
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64Fluorescence; Phosphorescence
    • G01N21/6408Fluorescence; Phosphorescence with measurement of decay time, time resolved fluorescence
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64Fluorescence; Phosphorescence
    • G01N21/645Specially adapted constructive features of fluorimeters
    • G01N21/6452Individual samples arranged in a regular 2D-array, e.g. multiwell plates
    • G01N21/6454Individual samples arranged in a regular 2D-array, e.g. multiwell plates using an integrated detector array
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64Fluorescence; Phosphorescence
    • G01N21/645Specially adapted constructive features of fluorimeters
    • G01N21/648Specially adapted constructive features of fluorimeters using evanescent coupling or surface plasmon coupling for the excitation of fluorescence

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Immunology (AREA)
  • Organic Chemistry (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Pathology (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Optics & Photonics (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • General Physics & Mathematics (AREA)
  • Data Mining & Analysis (AREA)
  • Investigating, Analyzing Materials By Fluorescence Or Luminescence (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Burglar Alarm Systems (AREA)
BR112018074572-3A 2016-06-01 2017-06-01 Métodos de identificação de nucleotídeos e para calibrar um instrumento de sequenciamento, meio de armazenamento legível em computador não transitório, dispositivo e instrumento de sequenciamento BR112018074572B1 (pt)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662343997P 2016-06-01 2016-06-01
US62/343,997 2016-06-01
PCT/US2017/035420 WO2017210413A1 (en) 2016-06-01 2017-06-01 Pulse caller and base caller

Publications (2)

Publication Number Publication Date
BR112018074572A2 BR112018074572A2 (pt) 2019-03-12
BR112018074572B1 true BR112018074572B1 (pt) 2024-02-27

Family

ID=59055317

Family Applications (1)

Application Number Title Priority Date Filing Date
BR112018074572-3A BR112018074572B1 (pt) 2016-06-01 2017-06-01 Métodos de identificação de nucleotídeos e para calibrar um instrumento de sequenciamento, meio de armazenamento legível em computador não transitório, dispositivo e instrumento de sequenciamento

Country Status (11)

Country Link
US (2) US10711299B2 (https=)
EP (2) EP4009330A1 (https=)
JP (1) JP6931665B2 (https=)
KR (1) KR102425257B1 (https=)
CN (1) CN109313925B (https=)
AU (1) AU2017274412B2 (https=)
BR (1) BR112018074572B1 (https=)
CA (1) CA3026061A1 (https=)
MX (1) MX2018014856A (https=)
TW (1) TWI755400B (https=)
WO (1) WO2017210413A1 (https=)

Families Citing this family (33)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3471402B1 (en) 2014-08-08 2023-05-31 Quantum-Si Incorporated Integrated device for temporal binning of received photons
KR20180111999A (ko) 2016-02-17 2018-10-11 테서렉트 헬스, 인코포레이티드 수명 촬상 및 검출 응용을 위한 센서 및 디바이스
EP4113104A3 (en) 2016-06-01 2023-02-22 Quantum-si Incorporated Integrated device for detecting and analyzing molecules
BR112019012414A2 (pt) 2016-12-19 2020-02-27 Quantum-Si Incorporated Carregamento de moléculas em poços de amostra para análise
CA3047826A1 (en) 2016-12-22 2018-06-28 Quantum-Si Incorporated Integrated photodetector with direct binning pixel
US11120104B2 (en) 2017-03-01 2021-09-14 Stmicroelectronics (Research & Development) Limited Method and apparatus for processing a histogram output from a detector sensor
KR102709865B1 (ko) 2017-05-05 2024-09-26 퀀텀-에스아이 인코포레이티드 생물학적 반응에 있어서 개질된 표면 반응성 및 오손방지 특성을 갖는 기재
US11378544B2 (en) 2018-01-08 2022-07-05 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
NL2020621B1 (en) 2018-01-08 2019-07-15 Illumina Inc Multiplexing of an active sensor detector using structured illumination
KR102239487B1 (ko) 2018-01-08 2021-04-14 일루미나, 인코포레이티드 반도체-기반 검출을 사용한 고-처리율 서열분석
WO2019147904A1 (en) * 2018-01-26 2019-08-01 Quantum-Si Incorporated Machine learning enabled pulse and base calling for sequencing devices
CN119364214A (zh) 2018-06-22 2025-01-24 宽腾矽公司 具有不同检测时间的电荷存储仓的集成光电检测器
AU2019330042A1 (en) * 2018-08-29 2021-03-11 Quantum-Si Incorporated System and methods for detecting lifetime using photon counting photodetectors
US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
US11783917B2 (en) 2019-03-21 2023-10-10 Illumina, Inc. Artificial intelligence-based base calling
US11423306B2 (en) 2019-05-16 2022-08-23 Illumina, Inc. Systems and devices for characterization and performance analysis of pixel-based sequencing
US11593649B2 (en) 2019-05-16 2023-02-28 Illumina, Inc. Base calling using convolutions
US11712715B2 (en) 2019-10-11 2023-08-01 Quantum-Si Incorporated Surface modification in the vapor phase
AU2021208557A1 (en) 2020-01-14 2022-09-01 Quantum-Si Incorporated Sensor for lifetime plus spectral characterization
WO2021146473A1 (en) 2020-01-14 2021-07-22 Quantum-Si Incorporated Integrated sensor for lifetime characterization
US12591780B2 (en) 2020-02-20 2026-03-31 Illumina, Inc. Data compression for artificial intelligence-based base calling
US12592298B2 (en) 2020-02-20 2026-03-31 Illumina, Inc. Hardware execution and acceleration of artificial intelligence-based base caller
CN121034400A (zh) 2020-02-20 2025-11-28 因美纳有限公司 基于人工智能的多对多碱基判读
US12354008B2 (en) 2020-02-20 2025-07-08 Illumina, Inc. Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
TW202147591A (zh) * 2020-03-02 2021-12-16 美商寬騰矽公司 用於多維信號分析之整合感應器
KR20220165754A (ko) 2020-04-08 2022-12-15 퀀텀-에스아이 인코포레이티드 스큐가 감소된 통합 센서
US20220065785A1 (en) * 2020-07-23 2022-03-03 Quantum-Si Incorporated System and method for detecting change points
CA3199745A1 (en) * 2020-10-27 2022-05-05 Quantum-Si Incorporated Calibration of single-molecule detection system
US12525320B2 (en) 2021-03-16 2026-01-13 Illumina, Inc. Neural network parameter quantization for base calling
US12217829B2 (en) 2021-04-15 2025-02-04 Illumina, Inc. Artificial intelligence-based analysis of protein three-dimensional (3D) structures
US12444482B2 (en) 2021-04-15 2025-10-14 Illumina, Inc. Multi-channel protein voxelization to predict variant pathogenicity using deep convolutional neural networks
US12530882B2 (en) 2021-07-01 2026-01-20 Illumina, Inc. Efficient artificial intelligence-based base calling of index sequences
WO2023137051A2 (en) 2022-01-12 2023-07-20 Quantum-Si Incorporated Integrated sensor

Family Cites Families (27)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2155186A1 (en) * 1993-02-01 1994-08-18 Kevin M. Ulmer Methods and apparatus for dna sequencing
DE19744490A1 (de) * 1997-10-08 1999-04-15 Temp Rite International Gmbh Trinkwasseraufbereitungsanlage
JP4566299B2 (ja) * 1998-04-09 2010-10-20 シスメックス株式会社 赤芽球の分類計数方法
WO2000009753A1 (en) * 1998-08-11 2000-02-24 Caliper Technologies Corp. Methods and systems for sequencing dna by distinguishing the decay times of fluorescent probes
DE19844931C1 (de) * 1998-09-30 2000-06-15 Stefan Seeger Verfahren zur DNS- oder RNS-Sequenzierung
US7056661B2 (en) * 1999-05-19 2006-06-06 Cornell Research Foundation, Inc. Method for sequencing nucleic acid molecules
GB2382648B (en) * 2001-12-11 2003-11-12 Amersham Pharm Biotech Uk Ltd System and method for time correlated multi-photon counting measurements
WO2005120204A2 (en) * 2004-06-07 2005-12-22 The Regents Of The University Of California Method for single molecule fluorescence analysis
CA2689626C (en) * 2007-06-06 2016-10-25 Pacific Biosciences Of California, Inc. Methods and processes for calling bases in sequence by incorporation methods
JP5643650B2 (ja) 2007-11-21 2014-12-17 コスモシド・インコーポレーテッド ゲノム同定システム
US20110165652A1 (en) * 2008-01-14 2011-07-07 Life Technologies Corporation Compositions, methods and systems for single molecule sequencing
CA2767521A1 (en) * 2009-07-10 2011-01-13 Perkinelmer Health Sciences, Inc. Detecting multinucleotide repeats
US9670243B2 (en) * 2010-06-02 2017-06-06 Industrial Technology Research Institute Compositions and methods for sequencing nucleic acids
US20140235474A1 (en) * 2011-06-24 2014-08-21 Sequenom, Inc. Methods and processes for non invasive assessment of a genetic variation
US9145623B2 (en) 2011-07-20 2015-09-29 Thermo Fisher Scientific Oy Transposon nucleic acids comprising a calibration sequence for DNA sequencing
JP5790242B2 (ja) * 2011-07-25 2015-10-07 富士ゼロックス株式会社 故障予測装置及びプログラム
CA2867489A1 (en) * 2012-03-30 2013-10-03 Pacific Biosciences Of California, Inc. Methods and composition for sequencing modified nucleic acids
CA2877094A1 (en) 2012-06-18 2013-12-27 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
HK1221053A1 (zh) * 2013-05-23 2017-05-19 艾弗诺泰普有限责任公司 用於保持或改善健康的方法和系统
WO2015074001A1 (en) * 2013-11-17 2015-05-21 Quantum-Si Incorporated Optical system and assay chip for probing, detecting and analyzing molecules
EP3084002A4 (en) 2013-12-16 2017-08-23 Complete Genomics, Inc. Basecaller for dna sequencing using machine learning
CN106462670B (zh) 2014-05-12 2020-04-10 豪夫迈·罗氏有限公司 超深度测序中的罕见变体召集
CA2957543A1 (en) 2014-08-08 2016-02-11 Quantum-Si Incorporated Optical system and assay chip for probing, detecting and analyzing molecules
EP3471402B1 (en) 2014-08-08 2023-05-31 Quantum-Si Incorporated Integrated device for temporal binning of received photons
EP4421188A3 (en) 2014-08-08 2024-10-23 Quantum-Si Incorporated Integrated device with external light source for probing, detecting, and analyzing molecules
US10185803B2 (en) 2015-06-15 2019-01-22 Deep Genomics Incorporated Systems and methods for classifying, prioritizing and interpreting genetic variants and therapies using a deep neural network
US9922285B1 (en) 2017-07-13 2018-03-20 HumanCode, Inc. Predictive assignments that relate to genetic information and leverage machine learning models

Also Published As

Publication number Publication date
US20170349944A1 (en) 2017-12-07
TW201800739A (zh) 2018-01-01
CN109313925A (zh) 2019-02-05
EP4009330A1 (en) 2022-06-08
JP2019529865A (ja) 2019-10-17
CN109313925B (zh) 2022-09-02
MX2018014856A (es) 2019-03-07
KR20190015371A (ko) 2019-02-13
AU2017274412B2 (en) 2022-07-21
KR102425257B1 (ko) 2022-07-27
BR112018074572A2 (pt) 2019-03-12
EP3465503B1 (en) 2021-09-29
AU2017274412A1 (en) 2018-12-06
WO2017210413A1 (en) 2017-12-07
JP6931665B2 (ja) 2021-09-08
US10711299B2 (en) 2020-07-14
US20200291467A1 (en) 2020-09-17
CA3026061A1 (en) 2017-12-07
EP3465503A1 (en) 2019-04-10
TWI755400B (zh) 2022-02-21

Similar Documents

Publication Publication Date Title
BR112018074572B1 (pt) Métodos de identificação de nucleotídeos e para calibrar um instrumento de sequenciamento, meio de armazenamento legível em computador não transitório, dispositivo e instrumento de sequenciamento
US12469581B2 (en) Machine learning enabled pulse and base calling for sequencing devices
RU2736384C1 (ru) Секвенирование с помощью одиночного источника света и двух оптических каналов
KR102515638B1 (ko) 뉴클레오타이드 서열분석 데이터의 이차 분석을 위한 시스템 및 방법
ES2808824T3 (es) Métodos y sistemas para analizar datos de imagen
BR112021003074A2 (pt) técnicas de fabricação de poço de amostra e estruturas para dispositivos de sensor integrado
US20250231172A1 (en) Single molecule multi-molecular trace methods and systems
BR112021009040A2 (pt) técnicas de fabricação de poço de amostra e estruturas para dispositivos sensores integrados
HK40076887A (en) Pulse caller and base caller
HK40005779B (en) Pulse caller and base caller
KR20260054069A (ko) 통합 센서 디바이스들을 위한 샘플 웰 제작 기술들 및 구조물들

Legal Events

Date Code Title Description
B350 Update of information on the portal [chapter 15.35 patent gazette]
B06W Patent application suspended after preliminary examination (for patents with searches from other patent authorities) chapter 6.23 patent gazette]
B09A Decision: intention to grant [chapter 9.1 patent gazette]
B15K Others concerning applications: alteration of classification

Free format text: A CLASSIFICACAO ANTERIOR ERA: G06F 19/22

Ipc: C12Q 1/68 (2018.01), G01N 21/64 (2006.01), G16B 30

B16A Patent or certificate of addition of invention granted [chapter 16.1 patent gazette]

Free format text: PRAZO DE VALIDADE: 20 (VINTE) ANOS CONTADOS A PARTIR DE 01/06/2017, OBSERVADAS AS CONDICOES LEGAIS

B21F Lapse acc. art. 78, item iv - on non-payment of the annual fees in time

Free format text: REFERENTE A 9A ANUIDADE.