CA3093971A1 - Tissue-specific methylation marker - Google Patents

Tissue-specific methylation marker Download PDF

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Publication number
CA3093971A1
CA3093971A1 CA3093971A CA3093971A CA3093971A1 CA 3093971 A1 CA3093971 A1 CA 3093971A1 CA 3093971 A CA3093971 A CA 3093971A CA 3093971 A CA3093971 A CA 3093971A CA 3093971 A1 CA3093971 A1 CA 3093971A1
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CA
Canada
Prior art keywords
tissue
methylation
cancer
target sequence
seq
Prior art date
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Pending
Application number
CA3093971A
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English (en)
French (fr)
Inventor
Yuk-Ming Dennis Lo
Rossa Wai Kwun Chiu
Kwan Chee Chan
Wanxia GAI
Lu JI
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.)
Grail Inc
Original Assignee
Grail 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 Grail Inc filed Critical Grail Inc
Publication of CA3093971A1 publication Critical patent/CA3093971A1/en
Pending legal-status Critical Current

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    • 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
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6823—Release of bound 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
    • 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
    • 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
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/30—Drug targeting using structural data; Docking or binding prediction
    • 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
    • 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
    • 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
    • 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
    • C12Q2600/112—Disease subtyping, staging or classification
    • 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
    • C12Q2600/118—Prognosis of disease development
    • 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
    • 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
    • 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
    • C12Q2600/158—Expression 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
    • C12Q2600/172—Haplotypes

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Pathology (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA3093971A 2018-03-15 2019-03-15 Tissue-specific methylation marker Pending CA3093971A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201862643649P 2018-03-15 2018-03-15
US62/643,649 2018-03-15
US201862769928P 2018-11-20 2018-11-20
US62/769,928 2018-11-20
PCT/US2019/022504 WO2019178496A1 (en) 2018-03-15 2019-03-15 Tissue-specific methylation marker

Publications (1)

Publication Number Publication Date
CA3093971A1 true CA3093971A1 (en) 2019-09-19

Family

ID=67908065

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3093971A Pending CA3093971A1 (en) 2018-03-15 2019-03-15 Tissue-specific methylation marker

Country Status (11)

Country Link
US (2) US11884966B2 (https=)
EP (1) EP3766076A4 (https=)
JP (2) JP7620803B2 (https=)
CN (2) CN119955906A (https=)
AU (1) AU2019233897B2 (https=)
CA (1) CA3093971A1 (https=)
IL (1) IL277306A (https=)
PH (1) PH12020551712A1 (https=)
SG (1) SG11202008957VA (https=)
TW (1) TWI848941B (https=)
WO (1) WO2019178496A1 (https=)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2019233897B2 (en) 2018-03-15 2024-10-24 Grail, Inc. Tissue-specific methylation marker
KR102103885B1 (ko) * 2019-10-08 2020-04-24 주식회사 레피다인 생물학적 시료의 간 조직 유래 여부를 판별하는 방법
KR102155044B1 (ko) * 2019-10-08 2020-09-11 주식회사 레피다인 생물학적 시료의 간암 조직 기원 여부를 판별하는 방법
EP4083232A4 (en) * 2019-12-26 2024-03-20 Anchordx Medical Co., Ltd. COMBINATION OF DNA METHYLATION BIOMARKERS, AND ITS DETECTION METHOD AND ASSOCIATED KIT
GB2612447B (en) * 2020-04-24 2025-08-13 Univ Cornell Methods for detecting tissue damage, graft versus host disease, and infections using cell-free DNA profiling
JP7646850B2 (ja) 2021-02-09 2025-03-17 エフ． ホフマン－ラ ロシュ アーゲー 核酸中のメチル化の塩基レベル検出のための方法
WO2023144704A1 (en) * 2022-01-25 2023-08-03 Gene Solutions Joint Stock Company Systems and methods for detecting tumor dna in mammalian blood
US20250361549A1 (en) 2022-06-14 2025-11-27 Roche Sequencing Solutions, Inc. Detection of epigenetic cytosine modification
WO2024112741A1 (en) * 2022-11-23 2024-05-30 Salk Institute For Biological Studies Dna methylation barcodes for identifying brain cells
CN117476222B (zh) * 2023-09-28 2024-10-25 上海交通大学医学院附属瑞金医院 一种肠癌肝转移的风险预测方法、系统和电子设备

Family Cites Families (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105243295B (zh) 2010-11-30 2018-08-17 香港中文大学 与癌症相关的遗传或分子畸变的检测
US9732390B2 (en) * 2012-09-20 2017-08-15 The Chinese University Of Hong Kong Non-invasive determination of methylome of fetus or tumor from plasma
SI4056712T1 (sl) * 2012-09-20 2024-10-30 The Chinese University Of Hong Kong Neinvazivno določanje metiloma tumorja iz plazme
US20160340740A1 (en) 2014-01-30 2016-11-24 The Regents Of The University Of California Methylation haplotyping for non-invasive diagnosis (monod)
WO2015159292A2 (en) * 2014-04-14 2015-10-22 Yissum Research Development Company Of The Hebrew University Of Jerusalem Ltd. A method and kit for determining the tissue or cell origin of dna
JP6681841B2 (ja) 2014-05-09 2020-04-15 ライフコーデックス アーゲー 特別な細胞タイプに由来するｄｎａの検出とそれに関連する方法
EP2942400A1 (en) 2014-05-09 2015-11-11 Lifecodexx AG Multiplex detection of DNA that originates from a specific cell-type
CA2951141C (en) 2014-06-04 2021-11-30 Quest Diagnostics Investments Incorporated Methylated markers for colorectal cancer
TWI813141B (zh) 2014-07-18 2023-08-21 香港中文大學 Ｄｎａ混合物中之組織甲基化模式分析
CA3183545C (en) * 2014-12-12 2026-01-13 Exact Sciences Corporation Compositions and methods for performing methylation detection assays
DK3408407T3 (da) 2016-01-29 2021-02-08 Epigenomics Ag Fremgangsmåder til påvisning af cpg-methylering af tumorafledt dna i blodprøver
CN110168099B (zh) 2016-06-07 2024-06-07 加利福尼亚大学董事会 用于疾病和病症分析的无细胞dna甲基化模式
AU2019233897B2 (en) 2018-03-15 2024-10-24 Grail, Inc. Tissue-specific methylation marker

Also Published As

Publication number Publication date
TWI848941B (zh) 2024-07-21
CN112534506B (zh) 2025-03-04
KR20210023804A (ko) 2021-03-04
EP3766076A4 (en) 2021-12-29
US11884966B2 (en) 2024-01-30
TW202010845A (zh) 2020-03-16
PH12020551712A1 (en) 2021-06-21
US20240191282A1 (en) 2024-06-13
CN119955906A (zh) 2025-05-09
SG11202008957VA (en) 2020-10-29
JP7620803B2 (ja) 2025-01-24
EP3766076A1 (en) 2021-01-20
AU2019233897A1 (en) 2020-10-22
AU2019233897B2 (en) 2024-10-24
CN112534506A (zh) 2021-03-19
IL277306A (en) 2020-10-29
JP2024156679A (ja) 2024-11-06
WO2019178496A1 (en) 2019-09-19
JP2021518107A (ja) 2021-08-02
US20190390257A1 (en) 2019-12-26

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