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 (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)

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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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BR112020014542A2 (pt) 2018-01-26 2020-12-08 Quantum-Si Incorporated Aprendizado de máquina habilitado por aplicação de pulso e de base para dispositivos de sequenciamento
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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
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AU2021208557A1 (en) 2020-01-14 2022-09-01 Quantum-Si Incorporated Sensor for lifetime plus spectral characterization
CA3168138A1 (en) 2020-01-14 2021-07-22 Quantum-Si Incorporated Integrated sensor for lifetime characterization
US12354008B2 (en) 2020-02-20 2025-07-08 Illumina, Inc. Knowledge distillation and gradient pruning-based compression of artificial intelligence-based base caller
US12592298B2 (en) 2020-02-20 2026-03-31 Illumina, Inc. Hardware execution and acceleration of artificial intelligence-based base caller
JP7747643B2 (ja) 2020-02-20 2025-10-01 イルミナ インコーポレイテッド 人工知能ベースの多対多ベースコール
US12591780B2 (en) 2020-02-20 2026-03-31 Illumina, Inc. Data compression for artificial intelligence-based base calling
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
AU2021372456A1 (en) * 2020-10-27 2023-06-08 Quantum-Si Incorporated Calibration of single-molecule detection system
US20220301657A1 (en) 2021-03-16 2022-09-22 Illumina, Inc. Tile location and/or cycle based weight set selection for base calling
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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
EP3465503A1 (en) 2019-04-10
MX2018014856A (es) 2019-03-07
KR102425257B1 (ko) 2022-07-27
CA3026061A1 (en) 2017-12-07
CN109313925A (zh) 2019-02-05
KR20190015371A (ko) 2019-02-13
EP3465503B1 (en) 2021-09-29
US20170349944A1 (en) 2017-12-07
US20200291467A1 (en) 2020-09-17
US10711299B2 (en) 2020-07-14
CN109313925B (zh) 2022-09-02
TWI755400B (zh) 2022-02-21
JP6931665B2 (ja) 2021-09-08
JP2019529865A (ja) 2019-10-17
EP4009330A1 (en) 2022-06-08
BR112018074572B1 (pt) 2024-02-27
TW201800739A (zh) 2018-01-01
BR112018074572A2 (pt) 2019-03-12
AU2017274412A1 (en) 2018-12-06
WO2017210413A1 (en) 2017-12-07

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