KR102425257B1 - 펄스 호출자 및 베이스 호출자 - Google Patents

펄스 호출자 및 베이스 호출자 Download PDF

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KR102425257B1
KR102425257B1 KR1020187037813A KR20187037813A KR102425257B1 KR 102425257 B1 KR102425257 B1 KR 102425257B1 KR 1020187037813 A KR1020187037813 A KR 1020187037813A KR 20187037813 A KR20187037813 A KR 20187037813A KR 102425257 B1 KR102425257 B1 KR 102425257B1
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light
time
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points
nucleotide incorporation
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KR20190015371A (ko
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조나단 엠. 로스버그
크레이그 벵거
멜 데이비
키스 지. 파이프
지미 지아
브라이언 리드
브렛 제이. 자르파스
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퀀텀-에스아이 인코포레이티드
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    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • 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
    • G01N21/6428—Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes"
    • G01N2021/6439—Measuring 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
    • 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
    • G01N21/6408—Fluorescence; Phosphorescence with measurement of decay time, time resolved fluorescence
    • 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
    • G01N21/645—Specially adapted constructive features of fluorimeters
    • G01N21/6452—Individual samples arranged in a regular 2D-array, e.g. multiwell plates
    • G01N21/6454—Individual samples arranged in a regular 2D-array, e.g. multiwell plates using an integrated detector array
    • 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
    • G01N21/645—Specially adapted constructive features of fluorimeters
    • G01N21/648—Specially 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)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Zoology (AREA)
  • Biochemistry (AREA)
  • Wood Science & Technology (AREA)
  • Molecular Biology (AREA)
  • General Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Optics & Photonics (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Microbiology (AREA)
  • Pathology (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)
KR1020187037813A 2016-06-01 2017-06-01 펄스 호출자 및 베이스 호출자 Active KR102425257B1 (ko)

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
KR20190015371A KR20190015371A (ko) 2019-02-13
KR102425257B1 true KR102425257B1 (ko) 2022-07-27

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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)
TW (1) TWI755400B (enExample)
WO (1) WO2017210413A1 (enExample)

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 (5)

* 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
US20130023423A1 (en) 2011-07-20 2013-01-24 Finnzymes Oy Transposon nucleic acids comprising a calibration sequence for dna sequencing
US20150299767A1 (en) 2012-06-18 2015-10-22 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
WO2016022998A2 (en) * 2014-08-08 2016-02-11 Quantum-Si Incorporated Integrated device for temporal binning of received photons
US20160041095A1 (en) 2014-08-08 2016-02-11 Quantum-Si Incorporated Optical system and assay chip for probing, detecting and analyzing molecule

Family Cites Families (22)

* 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
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
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
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 (6)

* 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
US20130023423A1 (en) 2011-07-20 2013-01-24 Finnzymes Oy Transposon nucleic acids comprising a calibration sequence for dna sequencing
US20150299767A1 (en) 2012-06-18 2015-10-22 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
WO2016022998A2 (en) * 2014-08-08 2016-02-11 Quantum-Si Incorporated Integrated device for temporal binning of received photons
US20160041095A1 (en) 2014-08-08 2016-02-11 Quantum-Si Incorporated Optical system and assay chip for probing, detecting and analyzing molecule
US20160133668A1 (en) 2014-08-08 2016-05-12 Quantum-Si Incorporated Integrated device for temporal binning of received photons

Also Published As

Publication number Publication date
CN109313925A (zh) 2019-02-05
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
TWI755400B (zh) 2022-02-21
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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