CN111542616A - 脱氨引起的序列错误的纠正 - Google Patents

脱氨引起的序列错误的纠正 Download PDF

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Publication number
CN111542616A
CN111542616A CN201880085431.9A CN201880085431A CN111542616A CN 111542616 A CN111542616 A CN 111542616A CN 201880085431 A CN201880085431 A CN 201880085431A CN 111542616 A CN111542616 A CN 111542616A
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nucleic acid
variant
subset
variation
specified position
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CN201880085431.9A
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Chinese (zh)
Inventor
马尔辛·西科拉
安德鲁·肯尼迪
阿里尔·海莫维奇
达里娅·丘多瓦
史蒂芬·费尔克拉夫
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Guardant Health Inc
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Guardant Health Inc
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Publication of CN111542616A publication Critical patent/CN111542616A/zh
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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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • 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

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CN201880085431.9A 2017-11-03 2018-11-02 脱氨引起的序列错误的纠正 Pending CN111542616A (zh)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201762581609P 2017-11-03 2017-11-03
US62/581,609 2017-11-03
PCT/US2018/059056 WO2019090147A1 (en) 2017-11-03 2018-11-02 Correcting for deamination-induced sequence errors

Publications (1)

Publication Number Publication Date
CN111542616A true CN111542616A (zh) 2020-08-14

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CN201880085431.9A Pending CN111542616A (zh) 2017-11-03 2018-11-02 脱氨引起的序列错误的纠正

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US (3) US11008616B2 (https=)
EP (1) EP3704265A4 (https=)
JP (3) JP7304852B2 (https=)
CN (1) CN111542616A (https=)
CA (1) CA3079252A1 (https=)
WO (1) WO2019090147A1 (https=)

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4581625A1 (en) * 2022-08-29 2025-07-09 Foundation Medicine, Inc. Methods and systems for detecting tumor shedding

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CN101072882A (zh) * 2004-09-10 2007-11-14 塞昆纳姆股份有限公司 用于核酸长程序列分析的方法
CN102076871A (zh) * 2008-11-07 2011-05-25 财团法人工业技术研究院 精确序列信息及修饰碱基位置确定的方法
WO2013148400A1 (en) * 2012-03-30 2013-10-03 Pacific Biosciences Of California, Inc. Methods and composition for sequencing modified nucleic acids
US20140121116A1 (en) * 2012-10-31 2014-05-01 Counsyl, Inc. System and Methods for Detecting Genetic Variation
US20150066385A1 (en) * 2013-08-30 2015-03-05 10X Technologies, Inc. Sequencing methods
WO2015164432A1 (en) * 2014-04-21 2015-10-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
CN105408496A (zh) * 2013-03-15 2016-03-16 夸登特健康公司 检测稀有突变和拷贝数变异的系统和方法
CN106661631A (zh) * 2014-06-06 2017-05-10 康奈尔大学 使用组合的核酸酶、连接酶、聚合酶和测序反应识别和枚举核酸序列、表达、拷贝或dna甲基化变化的方法

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AU7089600A (en) * 1999-08-30 2001-03-26 U.S. Army Medical Research Institute Of Infectious Diseases Monoclonal antibodies and vaccines against epitopes on the ebola virus glycoprotein
WO2003046146A2 (en) 2001-11-28 2003-06-05 Applera Corporation Compositions and methods of selective nucleic acid isolation
US8835358B2 (en) 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
ES2523140T3 (es) * 2010-09-21 2014-11-21 Population Genetics Technologies Ltd. Aumento de la confianza en las identificaciones de alelos con el recuento molecular
WO2013138510A1 (en) * 2012-03-13 2013-09-19 Patel Abhijit Ajit Measurement of nucleic acid variants using highly-multiplexed error-suppressed deep sequencing
PT2828218T (pt) 2012-03-20 2020-11-11 Univ Washington Through Its Center For Commercialization Métodos para baixar a taxa de erro da sequenciação paralela massiva de adn utilizando sequenciação duplex de consensus
EP2677449A1 (en) * 2012-06-19 2013-12-25 Sjöblom, Tobias Method and device for efficient calculation of allele ratio confidence intervals and uses thereof
CN104781421B (zh) 2012-09-04 2020-06-05 夸登特健康公司 检测稀有突变和拷贝数变异的系统和方法
CA2905429A1 (en) * 2013-03-14 2014-10-02 Abbott Molecular Inc. Minimizing errors using uracil-dna-n-glycosylase
US9163284B2 (en) * 2013-08-09 2015-10-20 President And Fellows Of Harvard College Methods for identifying a target site of a Cas9 nuclease
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CN101072882A (zh) * 2004-09-10 2007-11-14 塞昆纳姆股份有限公司 用于核酸长程序列分析的方法
CN102076871A (zh) * 2008-11-07 2011-05-25 财团法人工业技术研究院 精确序列信息及修饰碱基位置确定的方法
WO2013148400A1 (en) * 2012-03-30 2013-10-03 Pacific Biosciences Of California, Inc. Methods and composition for sequencing modified nucleic acids
US20140121116A1 (en) * 2012-10-31 2014-05-01 Counsyl, Inc. System and Methods for Detecting Genetic Variation
CN105408496A (zh) * 2013-03-15 2016-03-16 夸登特健康公司 检测稀有突变和拷贝数变异的系统和方法
US20150066385A1 (en) * 2013-08-30 2015-03-05 10X Technologies, Inc. Sequencing methods
WO2015164432A1 (en) * 2014-04-21 2015-10-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
CN106661631A (zh) * 2014-06-06 2017-05-10 康奈尔大学 使用组合的核酸酶、连接酶、聚合酶和测序反应识别和枚举核酸序列、表达、拷贝或dna甲基化变化的方法

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Also Published As

Publication number Publication date
EP3704265A1 (en) 2020-09-09
US11718873B2 (en) 2023-08-08
JP7606554B2 (ja) 2024-12-25
JP2025028203A (ja) 2025-02-28
US20240141425A1 (en) 2024-05-02
CA3079252A1 (en) 2019-05-09
US20210395816A1 (en) 2021-12-23
US20200377941A1 (en) 2020-12-03
US11008616B2 (en) 2021-05-18
JP7304852B2 (ja) 2023-07-07
WO2019090147A1 (en) 2019-05-09
EP3704265A4 (en) 2021-09-29
JP2021502072A (ja) 2021-01-28
JP2023060046A (ja) 2023-04-27

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Application publication date: 20200814