CA3193183A1 - Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease - Google Patents

Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease

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Publication number
CA3193183A1
CA3193183A1 CA3193183A CA3193183A CA3193183A1 CA 3193183 A1 CA3193183 A1 CA 3193183A1 CA 3193183 A CA3193183 A CA 3193183A CA 3193183 A CA3193183 A CA 3193183A CA 3193183 A1 CA3193183 A1 CA 3193183A1
Authority
CA
Canada
Prior art keywords
subsample
dna
methylation
target region
region set
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
CA3193183A
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English (en)
French (fr)
Inventor
Andrew Kennedy
William J. GREENLEAF
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
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Filing date
Publication date
Application filed by Guardant Health Inc filed Critical Guardant Health Inc
Publication of CA3193183A1 publication Critical patent/CA3193183A1/en
Pending legal-status Critical Current

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    • 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
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • C—CHEMISTRY; METALLURGY
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    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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    • 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
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
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    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
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    • 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
    • C12Q1/683—Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
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    • 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
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    • C12N2800/00—Nucleic acids vectors
    • C12N2800/80—Vectors containing sites for inducing double-stranded breaks, e.g. meganuclease restriction sites
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • 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
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    • 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
    • C12Q2600/166—Oligonucleotides used as internal standards, controls or normalisation probes

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biomedical Technology (AREA)
  • Pathology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Medicinal Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA3193183A 2020-09-30 2021-09-29 Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease Pending CA3193183A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202063086000P 2020-09-30 2020-09-30
US63/086,000 2020-09-30
US202063105183P 2020-10-23 2020-10-23
US63/105,183 2020-10-23
PCT/US2021/071649 WO2022073012A1 (en) 2020-09-30 2021-09-29 Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease

Publications (1)

Publication Number Publication Date
CA3193183A1 true CA3193183A1 (en) 2022-04-07

Family

ID=78333328

Family Applications (2)

Application Number Title Priority Date Filing Date
CA3193183A Pending CA3193183A1 (en) 2020-09-30 2021-09-29 Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease
CA3193090A Pending CA3193090A1 (en) 2020-09-30 2021-09-29 Methods and systems to improve the signal to noise ratio of dna methylation partitioning assays

Family Applications After (1)

Application Number Title Priority Date Filing Date
CA3193090A Pending CA3193090A1 (en) 2020-09-30 2021-09-29 Methods and systems to improve the signal to noise ratio of dna methylation partitioning assays

Country Status (5)

Country Link
US (3) US20220154285A1 (https=)
EP (2) EP4222279A1 (https=)
JP (2) JP2023544720A (https=)
CA (2) CA3193183A1 (https=)
WO (2) WO2022073011A1 (https=)

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NL2033070B1 (en) * 2022-09-19 2024-03-25 Univ Twente Method for detecting CpG methylation in a DNA target sequence
JP2026501670A (ja) * 2023-01-04 2026-01-16 ナテラ， インコーポレイテッド メチル化標的ｄｎａ分子を増幅するための方法および組成物
WO2024159118A1 (en) * 2023-01-27 2024-08-02 The Regents Of The University Of California Methods of hyper- and hypo-methylation analysis for disease detection
WO2024211551A1 (en) 2023-04-06 2024-10-10 Glaxosmithkline Intellectual Property (No.4) Limited Methods for treating and monitoring cancer
EP4713480A1 (en) * 2023-05-19 2026-03-25 Nucleix Ltd. Detecting methylation changes in dna samples using restriction enzymes and high throughput sequencing
CN116926194A (zh) * 2023-06-29 2023-10-24 纳昂达(南京)生物科技有限公司 一种检测dna样本甲基化状态的方法
WO2025106807A1 (en) * 2023-11-16 2025-05-22 The Board Of Trustees Of The Leland Stanford Junior University Classification of samples using methylation enrichment
WO2025165106A1 (ko) * 2024-01-29 2025-08-07 주식회사 지씨지놈 핵산의 메틸화 마커 검출 방법

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Also Published As

Publication number Publication date
JP2023544721A (ja) 2023-10-25
JP2023544720A (ja) 2023-10-25
US20220154285A1 (en) 2022-05-19
WO2022073012A1 (en) 2022-04-07
US20220162670A1 (en) 2022-05-26
US11946106B2 (en) 2024-04-02
EP4222278A1 (en) 2023-08-09
WO2022073011A1 (en) 2022-04-07
EP4222279A1 (en) 2023-08-09
US20230130140A1 (en) 2023-04-27
CA3193090A1 (en) 2022-04-07

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