CA3079252A1 - Correcting for deamination-induced sequence errors - Google Patents

Correcting for deamination-induced sequence errors Download PDF

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Publication number
CA3079252A1
CA3079252A1 CA3079252A CA3079252A CA3079252A1 CA 3079252 A1 CA3079252 A1 CA 3079252A1 CA 3079252 A CA3079252 A CA 3079252A CA 3079252 A CA3079252 A CA 3079252A CA 3079252 A1 CA3079252 A1 CA 3079252A1
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CA
Canada
Prior art keywords
designated position
nucleic acids
variant
subset
nucleic acid
Prior art date
Legal status (The legal status 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 status listed.)
Pending
Application number
CA3079252A
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English (en)
French (fr)
Inventor
Marcin Sikora
Andrew Kennedy
Ariel JAIMOVICH
Darya CHUDOVA
Stephen Fairclough
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Guardant Health Inc
Original Assignee
Guardant Health 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 Guardant Health Inc filed Critical Guardant Health Inc
Publication of CA3079252A1 publication Critical patent/CA3079252A1/en
Pending legal-status Critical Current

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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
    • 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
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • 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)
CA3079252A 2017-11-03 2018-11-02 Correcting for deamination-induced sequence errors Pending CA3079252A1 (en)

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
CA3079252A1 true CA3079252A1 (en) 2019-05-09

Family

ID=66332356

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3079252A Pending CA3079252A1 (en) 2017-11-03 2018-11-02 Correcting for deamination-induced sequence errors

Country Status (6)

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

Families Citing this family (1)

* 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

Family Cites Families (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6582908B2 (en) 1990-12-06 2003-06-24 Affymetrix, Inc. Oligonucleotides
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
JP2008512129A (ja) * 2004-09-10 2008-04-24 セクエノム，インコーポレイティド 核酸の広範囲配列分析法
US8486630B2 (en) * 2008-11-07 2013-07-16 Industrial Technology Research Institute Methods for accurate sequence data and modified base position determination
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
CA2867489A1 (en) * 2012-03-30 2013-10-03 Pacific Biosciences Of California, Inc. Methods and composition for sequencing modified nucleic acids
EP2677449A1 (en) * 2012-06-19 2013-12-25 Sjöblom, Tobias Method and device for efficient calculation of allele ratio confidence intervals and uses thereof
US9092401B2 (en) * 2012-10-31 2015-07-28 Counsyl, Inc. System and methods for detecting genetic variation
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
CN114574581A (zh) * 2013-03-15 2022-06-03 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
US9163284B2 (en) * 2013-08-09 2015-10-20 President And Fellows Of Harvard College Methods for identifying a target site of a Cas9 nuclease
US10395758B2 (en) * 2013-08-30 2019-08-27 10X Genomics, Inc. Sequencing methods
WO2015164432A1 (en) * 2014-04-21 2015-10-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
EP4170044B1 (en) * 2014-06-06 2026-03-11 Cornell University Method for identification and enumeration of nucleic acid sequence, expression, copy, or dna methylation changes, using combined nuclease, ligase, polymerase, and sequencing reactions
CN107075730A (zh) 2014-09-12 2017-08-18 利兰·斯坦福青年大学托管委员会 循环核酸的鉴定及用途
GB201502374D0 (en) * 2015-02-13 2015-04-01 Prokyma Technologies Ltd Method and apparatus relating to treatment of a blood sample for sequencing of circulating tumour cells
WO2016149261A1 (en) * 2015-03-16 2016-09-22 Personal Genome Diagnostics, Inc. Systems and methods for analyzing nucleic acid
JP6675164B2 (ja) * 2015-07-28 2020-04-01 株式会社理研ジェネシス 変異判定方法、変異判定プログラムおよび記録媒体
CN116640847A (zh) * 2016-02-02 2023-08-25 夸登特健康公司 癌症进化检测和诊断
CN109511265B (zh) * 2016-05-16 2023-07-14 安可济控股有限公司 通过链鉴定改进测序的方法

Also Published As

Publication number Publication date
EP3704265A1 (en) 2020-09-09
US11718873B2 (en) 2023-08-08
CN111542616A (zh) 2020-08-14
JP7606554B2 (ja) 2024-12-25
JP2025028203A (ja) 2025-02-28
US20240141425A1 (en) 2024-05-02
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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