TWI755400B - 脈衝命名器及基質命名器、識別核苷酸之方法、校準定序儀器之方法、識別發生核苷酸併入事件之時間的方法、非暫時性電腦可讀儲存媒體、及定序儀器 - Google Patents

脈衝命名器及基質命名器、識別核苷酸之方法、校準定序儀器之方法、識別發生核苷酸併入事件之時間的方法、非暫時性電腦可讀儲存媒體、及定序儀器 Download PDF

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TWI755400B
TWI755400B TW106118155A TW106118155A TWI755400B TW I755400 B TWI755400 B TW I755400B TW 106118155 A TW106118155 A TW 106118155A TW 106118155 A TW106118155 A TW 106118155A TW I755400 B TWI755400 B TW I755400B
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nucleotide incorporation
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TW201800739A (zh
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強納森 M 羅斯伯格
奎格 萬格
梅爾 達維
凱斯 G 菲夫
喆 賈
布萊恩 瑞德
布雷特 J 葛雅爾法斯
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美商寬騰矽公司
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    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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"
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    • G16B45/00ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
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    • 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

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  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
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  • Proteomics, Peptides & Aminoacids (AREA)
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  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
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  • 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)
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TW106118155A 2016-06-01 2017-06-01 脈衝命名器及基質命名器、識別核苷酸之方法、校準定序儀器之方法、識別發生核苷酸併入事件之時間的方法、非暫時性電腦可讀儲存媒體、及定序儀器 TWI755400B (zh)

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US201662343997P 2016-06-01 2016-06-01
US62/343,997 2016-06-01

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TW201800739A TW201800739A (zh) 2018-01-01
TWI755400B true TWI755400B (zh) 2022-02-21

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US (2) US10711299B2 (enExample)
EP (2) EP4009330A1 (enExample)
JP (1) JP6931665B2 (enExample)
KR (1) KR102425257B1 (enExample)
CN (1) CN109313925B (enExample)
AU (1) AU2017274412B2 (enExample)
BR (1) BR112018074572B1 (enExample)
CA (1) CA3026061A1 (enExample)
MX (1) MX2018014856A (enExample)
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Families Citing this family (29)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3194935B1 (en) 2014-08-08 2018-10-31 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
KR102627237B1 (ko) * 2016-06-01 2024-01-23 퀀텀-에스아이 인코포레이티드 분자들을 검출 및 분석하기 위한 통합 디바이스
CA3046680A1 (en) 2016-12-19 2018-06-28 Quantum-Si Incorporated Loading molecules into sample wells for analysis
CN110168732B (zh) 2016-12-22 2024-03-08 宽腾矽公司 具有直接合并像素的整合式光电侦测器
US11120104B2 (en) 2017-03-01 2021-09-14 Stmicroelectronics (Research & Development) Limited Method and apparatus for processing a histogram output from a detector sensor
WO2018204810A1 (en) 2017-05-05 2018-11-08 Quantum-Si Incorporated Substrates having modified surface reactivity and antifouling properties in biological reactions
WO2019136376A1 (en) 2018-01-08 2019-07-11 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
AU2019205496B2 (en) 2018-01-08 2021-08-19 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
MX2020007904A (es) 2018-01-26 2020-09-07 Quantum Si Inc Llamado de pulso y base habilitado por maquina de aprendizaje para dispositivos de secuenciacion.
CA3108295A1 (en) 2018-06-22 2019-12-26 Quantum-Si Incorporated Integrated photodetector with charge storage bin of varied detection time
EP3844486A1 (en) * 2018-08-29 2021-07-07 Quantum-Si Incorporated System and methods for detecting lifetime using photon counting photodetectors
US11783917B2 (en) 2019-03-21 2023-10-10 Illumina, Inc. Artificial intelligence-based base calling
US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
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
AU2020364058A1 (en) 2019-10-11 2022-05-26 Quantum-Si Incorporated Surface modification in the vapor phase
US11869917B2 (en) 2020-01-14 2024-01-09 Quantum-Si Incorporated Integrated sensor for lifetime characterization
EP4088319A1 (en) 2020-01-14 2022-11-16 Quantum-si Incorporated Sensor for lifetime plus spectral characterization
US20210265016A1 (en) 2020-02-20 2021-08-26 Illumina, Inc. Data Compression for Artificial Intelligence-Based Base Calling
US12354008B2 (en) 2020-02-20 2025-07-08 Illumina, Inc. Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
US11749380B2 (en) 2020-02-20 2023-09-05 Illumina, Inc. Artificial intelligence-based many-to-many base calling
US11719639B2 (en) * 2020-03-02 2023-08-08 Quantum-Si Incorporated Integrated sensor for multi-dimensional signal analysis
WO2021207400A2 (en) 2020-04-08 2021-10-14 Quantum-Si Incorporated Integrated sensor with reduced skew
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
US12217829B2 (en) 2021-04-15 2025-02-04 Illumina, Inc. Artificial intelligence-based analysis of protein three-dimensional (3D) structures
US20220336057A1 (en) 2021-04-15 2022-10-20 Illumina, Inc. Efficient voxelization for deep learning

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090024331A1 (en) * 2007-06-06 2009-01-22 Pacific Biosciences Of California, Inc. Methods and processes for calling bases in sequence by incorporation methods
US20160133668A1 (en) * 2014-08-08 2016-05-12 Quantum-Si Incorporated Integrated device for temporal binning of received photons

Family Cites Families (25)

* 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
AU5479599A (en) 1998-08-11 2000-03-06 Caliper Technologies Corporation 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
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
WO2009091847A2 (en) * 2008-01-14 2009-07-23 Life Technologies Corporation Compositions, methods and systems for single molecule sequencing
ES2573092T3 (es) * 2009-07-10 2016-06-06 Perkinelmer Health Sciences, Inc. Detección de repeticiones de multinucleótido
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
AU2013240166A1 (en) * 2012-03-30 2014-10-30 Pacific Biosciences Of California, Inc. Methods and composition for sequencing modified nucleic acids
WO2013191775A2 (en) * 2012-06-18 2013-12-27 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
AU2014268417A1 (en) * 2013-05-23 2015-11-26 Iphenotype Llc Methods and systems for assisting persons, product providers and/or service providers
MX392471B (es) * 2013-11-17 2025-03-24 Quantum Si Inc Sistema optico y chip de ensayo para sondear, detectar y analizar moleculas
WO2015095066A1 (en) 2013-12-16 2015-06-25 Complete Genomics, Inc. Basecaller for dna sequencing using machine learning
EP3143537B1 (en) 2014-05-12 2023-03-01 Roche Diagnostics GmbH Rare variant calls in ultra-deep sequencing
KR102472061B1 (ko) 2014-08-08 2022-11-29 퀀텀-에스아이 인코포레이티드 분자들을 프로빙, 검출 및 분석하기 위한 광학계 및 검정 칩
BR112017002501B1 (pt) 2014-08-08 2022-06-07 Quantum-Si Incorporated Dispositivos integrados, sistemas, método de detecção de presença de molécula em amostra, método de formação de dispositivo integrado e método de análise de espécime
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

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090024331A1 (en) * 2007-06-06 2009-01-22 Pacific Biosciences Of California, Inc. Methods and processes for calling bases in sequence by incorporation methods
US20160133668A1 (en) * 2014-08-08 2016-05-12 Quantum-Si Incorporated Integrated device for temporal binning of received photons

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CN109313925A (zh) 2019-02-05
KR102425257B1 (ko) 2022-07-27
EP4009330A1 (en) 2022-06-08
BR112018074572B1 (pt) 2024-02-27
AU2017274412B2 (en) 2022-07-21
KR20190015371A (ko) 2019-02-13
EP3465503A1 (en) 2019-04-10
US20170349944A1 (en) 2017-12-07
CA3026061A1 (en) 2017-12-07
US20200291467A1 (en) 2020-09-17
MX2018014856A (es) 2019-03-07
BR112018074572A2 (pt) 2019-03-12
JP2019529865A (ja) 2019-10-17
EP3465503B1 (en) 2021-09-29
JP6931665B2 (ja) 2021-09-08
TW201800739A (zh) 2018-01-01
CN109313925B (zh) 2022-09-02
US10711299B2 (en) 2020-07-14
WO2017210413A1 (en) 2017-12-07
AU2017274412A1 (en) 2018-12-06

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