CA3119980A1 - Methods, compositions, and systems for improving recovery of nucleic acid molecules - Google Patents

Methods, compositions, and systems for improving recovery of nucleic acid molecules Download PDF

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Publication number
CA3119980A1
CA3119980A1 CA3119980A CA3119980A CA3119980A1 CA 3119980 A1 CA3119980 A1 CA 3119980A1 CA 3119980 A CA3119980 A CA 3119980A CA 3119980 A CA3119980 A CA 3119980A CA 3119980 A1 CA3119980 A1 CA 3119980A1
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CA
Canada
Prior art keywords
fragment size
sample
subset
size control
control molecules
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
CA3119980A
Other languages
English (en)
French (fr)
Inventor
Stefanie Ann Ward Mortimer
Dustin Howard HITE
Laura Michelle MELROY
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 CA3119980A1 publication Critical patent/CA3119980A1/en
Pending legal-status Critical Current

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Classifications

    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/514—Detection characterised by immobilisation to a surface characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Biomedical Technology (AREA)
  • Immunology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA3119980A 2018-12-20 2019-12-20 Methods, compositions, and systems for improving recovery of nucleic acid molecules Pending CA3119980A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201862783046P 2018-12-20 2018-12-20
US62/783,046 2018-12-20
PCT/US2019/068146 WO2020132628A1 (en) 2018-12-20 2019-12-20 Methods, compositions, and systems for improving recovery of nucleic acid molecules

Publications (1)

Publication Number Publication Date
CA3119980A1 true CA3119980A1 (en) 2020-06-25

Family

ID=69326689

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3119980A Pending CA3119980A1 (en) 2018-12-20 2019-12-20 Methods, compositions, and systems for improving recovery of nucleic acid molecules

Country Status (7)

Country Link
US (2) US20200232010A1 (https=)
EP (1) EP3898969A1 (https=)
JP (2) JP2022514010A (https=)
CN (1) CN113454218A (https=)
CA (1) CA3119980A1 (https=)
SG (1) SG11202104701XA (https=)
WO (1) WO2020132628A1 (https=)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN111944806A (zh) * 2020-07-30 2020-11-17 上海韦翰斯生物医药科技有限公司 一种高通量测序污染检测用分子标签组及其应用
JP2024513187A (ja) * 2021-03-29 2024-03-22 イルミナ インコーポレイテッド ライブラリー中のｄｎａ損傷を評価し、アンプリコンサイズバイアスを正規化するための組成物及び方法
CN118139987A (zh) 2021-09-23 2024-06-04 基因组检测合作社公司 用于cfrna和cftna靶向ngs测序的组合物和方法
CN115710751A (zh) * 2022-11-09 2023-02-24 石家庄冰缘医学检验实验室有限公司 一种多重pcr建库防止污染的方法

Family Cites Families (29)

* 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
US20030017081A1 (en) 1994-02-10 2003-01-23 Affymetrix, Inc. Method and apparatus for imaging a sample on a device
DE69528706T2 (de) 1994-08-19 2003-06-12 Pe Corp. (Ny), Foster City Gekoppeltes ampflikation- und ligationverfahren
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
US6969488B2 (en) 1998-05-22 2005-11-29 Solexa, Inc. System and apparatus for sequential processing of analytes
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US7501245B2 (en) 1999-06-28 2009-03-10 Helicos Biosciences Corp. Methods and apparatuses for analyzing polynucleotide sequences
US6818395B1 (en) 1999-06-28 2004-11-16 California Institute Of Technology Methods and apparatus for analyzing polynucleotide sequences
AU7537200A (en) 1999-09-29 2001-04-30 Solexa Ltd. Polynucleotide sequencing
ATE377093T1 (de) 2000-07-07 2007-11-15 Visigen Biotechnologies Inc Sequenzbestimmung in echtzeit
WO2003046146A2 (en) 2001-11-28 2003-06-05 Applera Corporation Compositions and methods of selective nucleic acid isolation
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
CA2579150C (en) 2004-09-17 2014-11-25 Pacific Biosciences Of California, Inc. Apparatus and method for analysis of molecules
US7170050B2 (en) 2004-09-17 2007-01-30 Pacific Biosciences Of California, Inc. Apparatus and methods for optical analysis of molecules
US7482120B2 (en) 2005-01-28 2009-01-27 Helicos Biosciences Corporation Methods and compositions for improving fidelity in a nucleic acid synthesis reaction
US7282337B1 (en) 2006-04-14 2007-10-16 Helicos Biosciences Corporation Methods for increasing accuracy of nucleic acid sequencing
US20120208711A1 (en) * 2009-10-02 2012-08-16 Centre For Addiction And Mental Health Method for Analysis of DNA Methylation Profiles of Cell-Free Circulating DNA in Bodily Fluids
US8835358B2 (en) 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
US20160040229A1 (en) 2013-08-16 2016-02-11 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number 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
WO2015073080A1 (en) * 2013-11-12 2015-05-21 Life Technologies Corporation Reagents and methods for sequencing
ES2660989T3 (es) 2013-12-28 2018-03-27 Guardant Health, Inc. Métodos y sistemas para detectar variantes genéticas
EP3502273B1 (en) * 2014-12-12 2020-07-08 Verinata Health, Inc. Cell-free dna fragment
JP6873921B2 (ja) * 2015-05-18 2021-05-19 カリウス・インコーポレイテッド 核酸の集団を濃縮するための組成物および方法
US10095831B2 (en) * 2016-02-03 2018-10-09 Verinata Health, Inc. Using cell-free DNA fragment size to determine copy number variations
EP3978627A1 (en) * 2016-03-25 2022-04-06 Karius, Inc. Methods using synthetic nucleic acid spike-ins
CA3023248A1 (en) * 2016-05-06 2017-11-09 Regents Of The University Of Minnesota Analytical standards and methods of using same
MX2019007444A (es) * 2016-12-22 2019-08-16 Guardant Health Inc Metodos y sistemas para analisis de moleculas de acido nucleico.

Also Published As

Publication number Publication date
EP3898969A1 (en) 2021-10-27
SG11202104701XA (en) 2021-06-29
JP2025106543A (ja) 2025-07-15
JP2022514010A (ja) 2022-02-09
CN113454218A (zh) 2021-09-28
US20260035743A1 (en) 2026-02-05
US20200232010A1 (en) 2020-07-23
WO2020132628A1 (en) 2020-06-25

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