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WO2024081769A3 - Methods and systems for detection of cancer based on dna methylation of specific cpg sites - Google Patents

Methods and systems for detection of cancer based on dna methylation of specific cpg sites Download PDF

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Publication number
WO2024081769A3
WO2024081769A3 PCT/US2023/076666 US2023076666W WO2024081769A3 WO 2024081769 A3 WO2024081769 A3 WO 2024081769A3 US 2023076666 W US2023076666 W US 2023076666W WO 2024081769 A3 WO2024081769 A3 WO 2024081769A3
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WO
WIPO (PCT)
Prior art keywords
cpg sites
methods
subject
systems
detection
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.)
Ceased
Application number
PCT/US2023/076666
Other languages
French (fr)
Other versions
WO2024081769A9 (en
WO2024081769A2 (en
Inventor
Mark R. Kennedy
Rachel Anne GREENSTEIN
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.)
Foundation Medicine Inc
Original Assignee
Foundation Medicine Inc
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Filing date
Publication date
Application filed by Foundation Medicine Inc filed Critical Foundation Medicine Inc
Publication of WO2024081769A2 publication Critical patent/WO2024081769A2/en
Publication of WO2024081769A3 publication Critical patent/WO2024081769A3/en
Publication of WO2024081769A9 publication Critical patent/WO2024081769A9/en
Anticipated expiration legal-status Critical
Ceased 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
    • C12Q1/6876—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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • 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

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Pathology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Methods for detecting disease in a subject are described. In some instances, the methods may comprise: receiving sequence read data for a plurality of sequence reads derived from a sample; determining a methylation fraction value for a plurality of CpG sites within each genomic region of a set of selected genomic regions based on the sequence read data; and performing a statistical analysis to compare a distribution of the methylation fraction values determined for a plurality of CpG sites within one or more selected genomic regions in the subject to a corresponding distribution of methylation fraction values determined for the plurality of CpG sites within one or more selected genomic regions for a plurality of healthy individuals, where a difference between the distribution of methylation fraction values determined for the subject and that determined for the plurality of healthy individuals is indicative of a presence of disease in the subject.
PCT/US2023/076666 2022-10-13 2023-10-12 Methods and systems for detection of cancer based on dna methylation of specific cpg sites Ceased WO2024081769A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202263415794P 2022-10-13 2022-10-13
US63/415,794 2022-10-13

Publications (3)

Publication Number Publication Date
WO2024081769A2 WO2024081769A2 (en) 2024-04-18
WO2024081769A3 true WO2024081769A3 (en) 2024-05-30
WO2024081769A9 WO2024081769A9 (en) 2025-03-13

Family

ID=90670347

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/076666 Ceased WO2024081769A2 (en) 2022-10-13 2023-10-12 Methods and systems for detection of cancer based on dna methylation of specific cpg sites

Country Status (1)

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WO (1) WO2024081769A2 (en)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20250246310A1 (en) * 2023-10-18 2025-07-31 Guardant Health, Inc. Genomic and methylation biomarkers for determining patient risk of heart disease and novel genomic and epigenomic drug targets to decrease risk of heart disease and/or improve patient outcome after myocardial infarction or cardiac injury
CN119785892B (en) * 2024-12-09 2025-10-21 博尔诚（北京）科技有限公司 A multimodal pan-cancer early prediction method, prediction device and electronic device based on cfDNA methylation

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20190050528A1 (en) * 2014-07-18 2019-02-14 The Chinese University Of Hong Kong Methylation pattern analysis of tissues in a dna mixture
US20190252041A1 (en) * 2015-06-15 2019-08-15 Deep Genomics Incorporated Systems and methods for classifying, prioritizing and interpreting genetic variants and therapies using a deep neural network
US20200239965A1 (en) * 2018-12-21 2020-07-30 Grail, Inc. Source of origin deconvolution based on methylation fragments in cell-free dna samples

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20190050528A1 (en) * 2014-07-18 2019-02-14 The Chinese University Of Hong Kong Methylation pattern analysis of tissues in a dna mixture
US20190252041A1 (en) * 2015-06-15 2019-08-15 Deep Genomics Incorporated Systems and methods for classifying, prioritizing and interpreting genetic variants and therapies using a deep neural network
US20200239965A1 (en) * 2018-12-21 2020-07-30 Grail, Inc. Source of origin deconvolution based on methylation fragments in cell-free dna samples

Also Published As

Publication number Publication date
WO2024081769A9 (en) 2025-03-13
WO2024081769A2 (en) 2024-04-18

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