BR112018074572A2 - chamador de pulsos e chamador de base - Google Patents

chamador de pulsos e chamador de base

Info

Publication number
BR112018074572A2
BR112018074572A2 BR112018074572-3A BR112018074572A BR112018074572A2 BR 112018074572 A2 BR112018074572 A2 BR 112018074572A2 BR 112018074572 A BR112018074572 A BR 112018074572A BR 112018074572 A2 BR112018074572 A2 BR 112018074572A2
Authority
BR
Brazil
Prior art keywords
characteristic
nucleotide incorporation
caller
nucleotide
temporal
Prior art date
Application number
BR112018074572-3A
Other languages
English (en)
Other versions
BR112018074572B1 (pt
Inventor
M. Rothberg Jonathan
wenger Craig
Davey Mel
G. Fife Keith
JIA Jimmy
Reed Brian
J. GYARFAS Brett
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

    • 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
    • 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
    • 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)
  • 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)
  • Wood Science & Technology (AREA)
  • Biochemistry (AREA)
  • Zoology (AREA)
  • Microbiology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Pathology (AREA)
  • General Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Optics & Photonics (AREA)
  • Molecular Biology (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)

Abstract

sistema e métodos para identificar nucleotídeos com base em dados adquiridos a partir de um sensor durante o sequenciamento de ácidos nucleicos. o método pode incluir obter características da luz detectada a partir de marcadores luminescentes associados aos nucleotídeos durante eventos de incorporação de nucleotídeos. as características podem incluir, para cada evento de incorporação de nucleotídeos, uma característica temporal da luz e uma característica de intensidade da luz. a característica temporal representa uma velocidade de declínio de uma probabilidade de emissão de fótons por um marcador luminescente após excitação. o método pode ainda incluir agrupar pontos que representam as características dos eventos de incorporação de nucleotídeos em grupos de pontos. os pontos individuais podem representar pelo menos a característica temporal e a característica de intensidade para um evento de incorporação de nucleotídeos correspondente. o método pode ainda incluir atribuir os grupos de pontos a nucleotídeos individuais.
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 true BR112018074572A2 (pt) 2019-03-12
BR112018074572B1 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 (pt)
EP (2) EP3465503B1 (pt)
JP (1) JP6931665B2 (pt)
KR (1) KR102425257B1 (pt)
CN (1) CN109313925B (pt)
AU (1) AU2017274412B2 (pt)
BR (1) BR112018074572B1 (pt)
CA (1) CA3026061A1 (pt)
MX (1) MX2018014856A (pt)
TW (1) TWI755400B (pt)
WO (1) WO2017210413A1 (pt)

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CA2957540A1 (en) 2014-08-08 2016-02-11 Quantum-Si Incorporated Integrated device for temporal binning of received photons
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US10731209B2 (en) 2016-12-19 2020-08-04 Quantum-Si Incorporated Loading molecules into sample wells for analysis
BR112019012540A2 (pt) 2016-12-22 2019-11-12 Quantum-Si Incorporated fotodetector integrado com pixel de acondicionamento direto
US11120104B2 (en) 2017-03-01 2021-09-14 Stmicroelectronics (Research & Development) Limited Method and apparatus for processing a histogram output from a detector sensor
MX2019013111A (es) 2017-05-05 2019-12-16 Quantum Si Inc Sustratos que tienen reactividad de superficie modificada y propiedades antiincrustantes en reacciones biologicas.
KR102370055B1 (ko) * 2018-01-08 2022-03-03 일루미나, 인코포레이티드 반도체-기반 검출을 사용하는 고-처리율 서열분석용 시스템 및 디바이스
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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.
EP3811610A1 (en) 2018-06-22 2021-04-28 Quantum-Si Incorporated Integrated photodetector with charge storage bin of varied detection time
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US11593649B2 (en) 2019-05-16 2023-02-28 Illumina, Inc. Base calling using convolutions
EP4028570A1 (en) 2019-10-11 2022-07-20 Quantum-Si Incorporated Surface modification in the vapor phase
CA3168138A1 (en) 2020-01-14 2021-07-22 Quantum-Si Incorporated Integrated sensor for lifetime characterization
TW202145595A (zh) 2020-01-14 2021-12-01 美商寬騰矽公司 用於壽命及光譜特性分析之感應器
AU2021224871A1 (en) 2020-02-20 2022-09-08 Illumina, Inc. Artificial intelligence-based many-to-many base calling
EP4111178A1 (en) * 2020-03-02 2023-01-04 Quantum-si Incorporated Integrated sensor for multi-dimensional signal analysis
EP4133524A2 (en) 2020-04-08 2023-02-15 Quantum-si Incorporated Integrated sensor with reduced skew
CA3199745A1 (en) * 2020-10-27 2022-05-05 Quantum-Si Incorporated Calibration of single-molecule detection system
US20220336054A1 (en) 2021-04-15 2022-10-20 Illumina, Inc. Deep Convolutional Neural Networks to Predict Variant Pathogenicity using Three-Dimensional (3D) Protein Structures

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Also Published As

Publication number Publication date
KR20190015371A (ko) 2019-02-13
JP6931665B2 (ja) 2021-09-08
TWI755400B (zh) 2022-02-21
TW201800739A (zh) 2018-01-01
AU2017274412A1 (en) 2018-12-06
JP2019529865A (ja) 2019-10-17
KR102425257B1 (ko) 2022-07-27
US20170349944A1 (en) 2017-12-07
CN109313925B (zh) 2022-09-02
EP3465503B1 (en) 2021-09-29
BR112018074572B1 (pt) 2024-02-27
AU2017274412B2 (en) 2022-07-21
EP3465503A1 (en) 2019-04-10
MX2018014856A (es) 2019-03-07
CA3026061A1 (en) 2017-12-07
CN109313925A (zh) 2019-02-05
US20200291467A1 (en) 2020-09-17
EP4009330A1 (en) 2022-06-08
US10711299B2 (en) 2020-07-14
WO2017210413A1 (en) 2017-12-07

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B06W Patent application suspended after preliminary examination (for patents with searches from other patent authorities) chapter 6.23 patent gazette]
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