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

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Classifications

    • 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
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring 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
    • 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"
    • 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
    • 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
    • G16B45/00ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • 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"
    • 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

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)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Organic Chemistry (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biochemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Optics & Photonics (AREA)
  • Pathology (AREA)
  • Genetics & Genomics (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Physics & Mathematics (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • General Engineering & Computer Science (AREA)
  • Data Mining & Analysis (AREA)
  • Investigating, Analyzing Materials By Fluorescence Or Luminescence (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Burglar Alarm Systems (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (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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US9759658B2 (en) 2014-08-08 2017-09-12 Quantum-Si Incorporated Integrated device for temporal binning of received photons
JP2019512090A (ja) 2016-02-17 2019-05-09 テッセラクト ヘルス インコーポレイテッドTesseract Health,Inc. 寿命イメージングおよび検出用途のためのセンサおよびデバイス
CN114674788A (zh) * 2016-06-01 2022-06-28 宽腾矽公司 用于检测及分析分子的集成装置
MX2019007247A (es) 2016-12-19 2019-08-16 Quantum Si Inc Carga de moleculas en pocillos para muestra para su analisis.
AU2017382316B2 (en) 2016-12-22 2023-02-09 Quantum-Si Incorporated Integrated photodetector with direct binning pixel
US11120104B2 (en) 2017-03-01 2021-09-14 Stmicroelectronics (Research & Development) Limited Method and apparatus for processing a histogram output from a detector sensor
EP3619323A4 (en) 2017-05-05 2021-01-27 Quantum-si Incorporated SUBSTRATES WITH MODIFIED SURFACE REACTIVITY AND ANTIFOULING PROPERTIES IN BIOLOGICAL REACTIONS
CA3065780A1 (en) 2018-01-08 2019-07-11 Illumina, Inc. Systems and devices for high-throughput sequencing with semiconductor-based detection
US11378544B2 (en) 2018-01-08 2022-07-05 Illumina, Inc. High-throughput sequencing with semiconductor-based detection
CA3088687A1 (en) * 2018-01-26 2019-08-01 Quantum-Si Incorporated Machine learning enabled pulse and base calling for sequencing devices
BR112020024790A2 (pt) 2018-06-22 2021-03-02 Quantum-Si Incorporated fotodetector integrado com região de armazenamento de carga de tempo de detecção variado
CN112930476A (zh) * 2018-08-29 2021-06-08 宽腾矽公司 使用光子计数光电检测器以检测寿命的系统及方法
US11347965B2 (en) 2019-03-21 2022-05-31 Illumina, Inc. Training data generation for artificial intelligence-based sequencing
US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
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
JP2023510578A (ja) 2020-01-14 2023-03-14 クアンタム-エスアイ インコーポレイテッド 寿命およびスペクトル特性評価用センサ
EP4107735A2 (en) 2020-02-20 2022-12-28 Illumina, Inc. Artificial intelligence-based many-to-many base calling
JP2023515682A (ja) * 2020-03-02 2023-04-13 クアンタム-エスアイ インコーポレイテッド 多次元信号解析用集積センサ
CN115769377A (zh) 2020-04-08 2023-03-07 宽腾矽公司 偏斜减小的集成传感器
US20220128566A1 (en) * 2020-10-27 2022-04-28 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
WO2017210413A1 (en) 2017-12-07
CN109313925A (zh) 2019-02-05
MX2018014856A (es) 2019-03-07
AU2017274412B2 (en) 2022-07-21
AU2017274412A1 (en) 2018-12-06
US10711299B2 (en) 2020-07-14
KR20190015371A (ko) 2019-02-13
JP2019529865A (ja) 2019-10-17
TWI755400B (zh) 2022-02-21
CA3026061A1 (en) 2017-12-07
EP4009330A1 (en) 2022-06-08
BR112018074572B1 (pt) 2024-02-27
CN109313925B (zh) 2022-09-02
US20170349944A1 (en) 2017-12-07
US20200291467A1 (en) 2020-09-17
EP3465503B1 (en) 2021-09-29
KR102425257B1 (ko) 2022-07-27
TW201800739A (zh) 2018-01-01
JP6931665B2 (ja) 2021-09-08
EP3465503A1 (en) 2019-04-10

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