CA3199829A1 - Compositions and methods for enriching methylated polynucleotides - Google Patents

Compositions and methods for enriching methylated polynucleotides

Info

Publication number
CA3199829A1
CA3199829A1 CA3199829A CA3199829A CA3199829A1 CA 3199829 A1 CA3199829 A1 CA 3199829A1 CA 3199829 A CA3199829 A CA 3199829A CA 3199829 A CA3199829 A CA 3199829A CA 3199829 A1 CA3199829 A1 CA 3199829A1
Authority
CA
Canada
Prior art keywords
dna
nucleobase
sample
modified
subsample
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
CA3199829A
Other languages
English (en)
French (fr)
Inventor
Andrew Kennedy
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 CA3199829A1 publication Critical patent/CA3199829A1/en
Pending legal-status Critical Current

Links

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
    • C12Q1/6876—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
    • 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
    • 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
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/50—Determining the risk of developing a disease

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biomedical Technology (AREA)
  • Pathology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA3199829A 2020-11-30 2021-11-30 Compositions and methods for enriching methylated polynucleotides Pending CA3199829A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202063119520P 2020-11-30 2020-11-30
US63/119,520 2020-11-30
PCT/US2021/061280 WO2022115810A1 (en) 2020-11-30 2021-11-30 Compositions and methods for enriching methylated polynucleotides

Publications (1)

Publication Number Publication Date
CA3199829A1 true CA3199829A1 (en) 2022-06-02

Family

ID=79164721

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3199829A Pending CA3199829A1 (en) 2020-11-30 2021-11-30 Compositions and methods for enriching methylated polynucleotides

Country Status (5)

Country Link
US (1) US20240150844A1 (https=)
EP (1) EP4251765A1 (https=)
JP (1) JP2023551292A (https=)
CA (1) CA3199829A1 (https=)
WO (1) WO2022115810A1 (https=)

Families Citing this family (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2024512156A (ja) * 2021-03-30 2024-03-18 レゾリューション バイオサイエンス， インコーポレイテッド 複数のライブラリーを同時に遺伝子解析するための組成物及び方法
EP4655416A1 (en) * 2023-01-25 2025-12-03 Guardant Health, Inc. Nucleic acid methylation profiling method
WO2025090956A1 (en) * 2023-10-26 2025-05-01 Guardant Health, Inc. Methods for detecting nucleic acid variants using capture probes
WO2025155895A1 (en) * 2024-01-19 2025-07-24 Guardant Health, Inc. Nucleic acid modification profiling method
GB2644427A (en) * 2024-07-23 2026-04-15 Tagomics Ltd Profiling method
WO2026024692A1 (en) * 2024-07-24 2026-01-29 Guardant Health, Inc. Direct methylation single-base resolution sequencing of enriched unmethylated dna

Family Cites Families (16)

* 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
AU2002359522A1 (en) 2001-11-28 2003-06-10 Applera Corporation Compositions and methods of selective nucleic acid isolation
CA2519860C (en) 2003-03-21 2018-01-16 Santaris Pharma A/S Short interfering rna (sirna) analogues
US8486630B2 (en) 2008-11-07 2013-07-16 Industrial Technology Research Institute Methods for accurate sequence data and modified base position determination
US20110237444A1 (en) * 2009-11-20 2011-09-29 Life Technologies Corporation Methods of mapping genomic methylation patterns
US8835358B2 (en) 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
EP2630257B1 (en) * 2010-10-22 2017-08-02 Oslo Universitetssykehus HF Methods and kits for detection of 5-hydroxymethylcytosine
GB2533006B (en) 2012-09-04 2017-06-07 Guardant Health Inc Systems and methods to detect copy number variation
CN107002122B (zh) 2014-07-25 2023-09-19 华盛顿大学 确定导致无细胞dna的产生的组织和/或细胞类型的方法以及使用其鉴定疾病或紊乱的方法
MX391039B (es) * 2016-04-07 2025-03-21 Univ Leland Stanford Junior Diagnostico no invasivo por medio de la secuenciacion del adn libre de celulas 5-hidroxi-metilado.
KR102610098B1 (ko) 2016-07-06 2023-12-04 가던트 헬쓰, 인크. 무세포 핵산의 프래그멘톰 프로파일링을 위한 방법
US9850523B1 (en) 2016-09-30 2017-12-26 Guardant Health, Inc. Methods for multi-resolution analysis of cell-free nucleic acids
CA3046007A1 (en) 2016-12-22 2018-06-28 Guardant Health, Inc. Methods and systems for analyzing nucleic acid molecules
WO2019160994A1 (en) * 2018-02-14 2019-08-22 Bluestar Genomics, Inc. Methods for the epigenetic analysis of dna, particularly cell-free dna
EP4567131A3 (en) * 2019-01-31 2025-09-03 Guardant Health, Inc. Compositions and methods for isolating cell-free dna

Also Published As

Publication number Publication date
WO2022115810A1 (en) 2022-06-02
US20240150844A1 (en) 2024-05-09
JP2023551292A (ja) 2023-12-07
EP4251765A1 (en) 2023-10-04

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