AU2017274412B2 - Pulse caller and base caller - Google Patents

Pulse caller and base caller Download PDF

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Publication number
AU2017274412B2
AU2017274412B2 AU2017274412A AU2017274412A AU2017274412B2 AU 2017274412 B2 AU2017274412 B2 AU 2017274412B2 AU 2017274412 A AU2017274412 A AU 2017274412A AU 2017274412 A AU2017274412 A AU 2017274412A AU 2017274412 B2 AU2017274412 B2 AU 2017274412B2
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AU
Australia
Prior art keywords
points
light
nucleotides
characteristic
intensity
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AU2017274412A
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AU2017274412A1 (en
Inventor
Mel DAVEY
Keith G. Fife
Brett J. Gyarfas
Jimmy Jia
Brian Reed
Jonathan M. Rothberg
Craig Wenger
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Quantum Si Inc
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Quantum Si Inc
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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

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)
AU2017274412A 2016-06-01 2017-06-01 Pulse caller and base caller Ceased AU2017274412B2 (en)

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
AU2017274412A1 AU2017274412A1 (en) 2018-12-06
AU2017274412B2 true AU2017274412B2 (en) 2022-07-21

Family

ID=59055317

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2017274412A Ceased AU2017274412B2 (en) 2016-06-01 2017-06-01 Pulse caller and base caller

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=)

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US11378544B2 (en) 2018-01-08 2022-07-05 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
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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
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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
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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
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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
US20170349944A1 (en) 2017-12-07
TW201800739A (zh) 2018-01-01
BR112018074572B1 (pt) 2024-02-27
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
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

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MK14 Patent ceased section 143(a) (annual fees not paid) or expired