BR112023026615A2 - Métrica de relação sinal-ruído para determinar chamadas de bases de nucleotídeos e qualidade de chamadas de bases - Google Patents

Métrica de relação sinal-ruído para determinar chamadas de bases de nucleotídeos e qualidade de chamadas de bases

Info

Publication number
BR112023026615A2
BR112023026615A2 BR112023026615A BR112023026615A BR112023026615A2 BR 112023026615 A2 BR112023026615 A2 BR 112023026615A2 BR 112023026615 A BR112023026615 A BR 112023026615A BR 112023026615 A BR112023026615 A BR 112023026615A BR 112023026615 A2 BR112023026615 A2 BR 112023026615A2
Authority
BR
Brazil
Prior art keywords
noise ratio
signal
generate
base calling
metrics
Prior art date
Application number
BR112023026615A
Other languages
English (en)
Inventor
Ali Kagalwalla Abde
Jon ojard Eric
S Vieceli John
Nitin Udpa
Rami Mehio
Original Assignee
Illumina Inc
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 Illumina Inc filed Critical Illumina Inc
Publication of BR112023026615A2 publication Critical patent/BR112023026615A2/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
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • 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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Bioethics (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Signal Processing (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Artificial Intelligence (AREA)
  • Databases & Information Systems (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

métrica de relação sinal-ruído para determinar chamadas de bases de nucleotídeos e qualidade de chamadas de bases. esta revelação descreve métodos, mídias não transitórias legíveis por computador e sistemas que podem gerar métricas de relação sinal-ruído para grupos de oligonucleotídeos aos quais são adicionadas bases de nucleotídeos marcadas e utilizar as métricas de relação sinal-ruído para gerar chamadas de bases de nucleotídeos e determinar a qualidade da chamada de bases. por exemplo, os sistemas revelados podem gerar as métricas de relação sinal-ruído usando fatores de escala e níveis de ruído associados a sinais de luz detectados dos grupos de oligonucleotídeos. os sistemas revelados podem utilizar as métricas de relação sinal-ruído para gerar limites de valor de intensidade para gerar chamadas de base de nucleotídeos para os sinais de acordo com um ou mais modelos de distribuição de chamadas de base. além disso, os sistemas revelados podem utilizar um limite para filtrar os sinais detectados dos grupos de oligonucleotídeos que têm métricas de relação sinal-ruído baixas. os sistemas revelados podem ainda utilizar as métricas de relação sinal-ruído para gerar métricas de qualidade para chamadas de bases de nucleotídeos geradas.
BR112023026615A 2021-06-29 2022-06-02 Métrica de relação sinal-ruído para determinar chamadas de bases de nucleotídeos e qualidade de chamadas de bases BR112023026615A2 (pt)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202163216401P 2021-06-29 2021-06-29
PCT/US2022/072737 WO2023278927A1 (en) 2021-06-29 2022-06-02 Signal-to-noise-ratio metric for determining nucleotide-base calls and base-call quality

Publications (1)

Publication Number Publication Date
BR112023026615A2 true BR112023026615A2 (pt) 2024-03-05

Family

ID=82483142

Family Applications (1)

Application Number Title Priority Date Filing Date
BR112023026615A BR112023026615A2 (pt) 2021-06-29 2022-06-02 Métrica de relação sinal-ruído para determinar chamadas de bases de nucleotídeos e qualidade de chamadas de bases

Country Status (9)

Country Link
US (1) US20220415442A1 (pt)
EP (1) EP4364154A1 (pt)
KR (1) KR20240022490A (pt)
CN (1) CN117730372A (pt)
AU (1) AU2022305321A1 (pt)
BR (1) BR112023026615A2 (pt)
CA (1) CA3224402A1 (pt)
IL (1) IL309308A (pt)
WO (1) WO2023278927A1 (pt)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN117497055B (zh) * 2024-01-02 2024-03-12 北京普译生物科技有限公司 神经网络模型训练、碱基测序电信号的片段化方法及装置

Family Cites Families (32)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0450060A1 (en) 1989-10-26 1991-10-09 Sri International Dna sequencing
US5846719A (en) 1994-10-13 1998-12-08 Lynx Therapeutics, Inc. Oligonucleotide tags for sorting and identification
US5750341A (en) 1995-04-17 1998-05-12 Lynx Therapeutics, Inc. DNA sequencing by parallel oligonucleotide extensions
GB9620209D0 (en) 1996-09-27 1996-11-13 Cemu Bioteknik Ab Method of sequencing DNA
GB9626815D0 (en) 1996-12-23 1997-02-12 Cemu Bioteknik Ab Method of sequencing DNA
DE69837913T2 (de) 1997-04-01 2008-02-07 Solexa Ltd., Saffron Walden Verfahren zur vervielfältigung von nukleinsäure
US6969488B2 (en) 1998-05-22 2005-11-29 Solexa, Inc. System and apparatus for sequential processing of analytes
US6274320B1 (en) 1999-09-16 2001-08-14 Curagen Corporation Method of sequencing a nucleic acid
US7001792B2 (en) 2000-04-24 2006-02-21 Eagle Research & Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
WO2002004680A2 (en) 2000-07-07 2002-01-17 Visigen Biotechnologies, Inc. Real-time sequence determination
US7211414B2 (en) 2000-12-01 2007-05-01 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
EP3795577A1 (en) 2002-08-23 2021-03-24 Illumina Cambridge Limited Modified nucleotides
GB0321306D0 (en) 2003-09-11 2003-10-15 Solexa Ltd Modified polymerases for improved incorporation of nucleotide analogues
EP2789383B1 (en) 2004-01-07 2023-05-03 Illumina Cambridge Limited Molecular arrays
JP2008513782A (ja) 2004-09-17 2008-05-01 パシフィック バイオサイエンシーズ オブ カリフォルニア， インコーポレイテッド 分子解析のための装置及び方法
WO2006064199A1 (en) 2004-12-13 2006-06-22 Solexa Limited Improved method of nucleotide detection
JP4990886B2 (ja) 2005-05-10 2012-08-01 ソレックサ リミテッド 改良ポリメラーゼ
GB0514936D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Preparation of templates for nucleic acid sequencing
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
EP3373174A1 (en) 2006-03-31 2018-09-12 Illumina, Inc. Systems and devices for sequence by synthesis analysis
AU2007309504B2 (en) 2006-10-23 2012-09-13 Pacific Biosciences Of California, Inc. Polymerase enzymes and reagents for enhanced nucleic acid sequencing
US8349167B2 (en) 2006-12-14 2013-01-08 Life Technologies Corporation Methods and apparatus for detecting molecular interactions using FET arrays
CA2672315A1 (en) 2006-12-14 2008-06-26 Ion Torrent Systems Incorporated Methods and apparatus for measuring analytes using large scale fet arrays
US8262900B2 (en) 2006-12-14 2012-09-11 Life Technologies Corporation Methods and apparatus for measuring analytes using large scale FET arrays
US20100137143A1 (en) 2008-10-22 2010-06-03 Ion Torrent Systems Incorporated Methods and apparatus for measuring analytes
US8951781B2 (en) 2011-01-10 2015-02-10 Illumina, Inc. Systems, methods, and apparatuses to image a sample for biological or chemical analysis
HRP20211523T1 (hr) 2011-09-23 2021-12-24 Illumina, Inc. Pripravci za sekvenciranje nukleinske kiseline
WO2013151622A1 (en) 2012-04-03 2013-10-10 Illumina, Inc. Integrated optoelectronic read head and fluidic cartridge useful for nucleic acid sequencing
EP3715467A1 (en) * 2013-12-03 2020-09-30 Illumina, Inc. Methods and systems for analyzing image data
US11538556B2 (en) * 2018-01-26 2022-12-27 Quantum-Si Incorporated Machine learning enabled pulse and base calling for sequencing devices
US11210554B2 (en) * 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata

Also Published As

Publication number Publication date
EP4364154A1 (en) 2024-05-08
US20220415442A1 (en) 2022-12-29
CA3224402A1 (en) 2023-01-05
IL309308A (en) 2024-02-01
CN117730372A (zh) 2024-03-19
WO2023278927A1 (en) 2023-01-05
KR20240022490A (ko) 2024-02-20
AU2022305321A1 (en) 2024-01-18

Similar Documents

Publication Publication Date Title
BR112023026615A2 (pt) Métrica de relação sinal-ruído para determinar chamadas de bases de nucleotídeos e qualidade de chamadas de bases
BR112019002215A2 (pt) seleção de nível de melhoramento de cobertura baseada em classe de potência
MX2019008347A (es) Secuenciamiento de canal bioptico, de una sola fuente de luz.
EA202090090A1 (ru) Включение неприродных нуклеотидов и способы с ними
MX2018009823A (es) Metodos y sistemas para la deteccion de cariotipos anormales.
BR112017018199A2 (pt) alocação de recurso de frequência para um sistema de internet celular de banda estreita, de coisas
BR112019016174A2 (pt) Fase de refinamento de feixe rápido para treinamento de formação de feixe periódico
MX2018010656A (es) Metodo y dispositivo para la determinacion de recursos de transmision para comunicaciones de dispositivo a dispositivo.
EA201100486A1 (ru) Лифтовая система
BR112016018143A2 (pt) Sistema de rastreamento de veículo configurado para instalação em um veículo que é um assinante de uma rede de rastreamento de veículo; e método para rastrear veículos
MX2019014685A (es) Metodo para determinar tonos reservados y transmisor para ejecutar reduccion papr utilizando la reservacion de tono.
MX2018012853A (es) Sistemas y metodos para la caracterizacion de convulsiones.
MX2020013229A (es) Endonucleasas cpf1 mutantes.
FR3095566B1 (fr) Reseau de communication comprenant des groupes de signalisation
MX2022010276A (es) Llamada de base de muchos a muchos basada en inteligencia artificial.
IN2015DN02441A (pt)
DE112020002482A5 (de) Beleuchtungsanordnung, lichtführungsanordnung und verfahren
PE20210109A1 (es) Moduladores de la expresion de irf4
JP2016531525A5 (pt)
BR112021022809A2 (pt) Método de sequenciamento de canal único baseado em autoluminescência
BR112018069885A2 (pt) método para detecção de pixels saturados em uma imagem
EA202192906A1 (ru) Ген, модифицирующий устойчивость к вирусу некротической желтой прожилки свеклы (bnyvv)
EA201800293A1 (ru) Альтернативные способы управления перекрестным сшиванием в ударопрочном полистироле
CL2021002138A1 (es) Dispositivo de codificación de video, método de codificación de video, programa de codificación de video, dispositivo de decodificación de video, método de decodificación de video y programa de decodificación de video.
BR112021025490A2 (pt) Protocolo de entrega reatribuído