EP4623096A4 - Fragmentomics-based identification of tumor-specific copy number changes in liquid biopsy - Google Patents

Fragmentomics-based identification of tumor-specific copy number changes in liquid biopsy

Info

Publication number
EP4623096A4
EP4623096A4 EP23895315.2A EP23895315A EP4623096A4 EP 4623096 A4 EP4623096 A4 EP 4623096A4 EP 23895315 A EP23895315 A EP 23895315A EP 4623096 A4 EP4623096 A4 EP 4623096A4
Authority
EP
European Patent Office
Prior art keywords
fragmentomics
tumor
copy number
number changes
based identification
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
EP23895315.2A
Other languages
German (de)
French (fr)
Other versions
EP4623096A1 (en
Inventor
Alexander D Fine
Brennan Decker
Zheng Kuang
Chang Xu
Daokun Sun
Yanmei Huang
Jason D Hughes
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
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 Foundation Medicine Inc filed Critical Foundation Medicine Inc
Publication of EP4623096A1 publication Critical patent/EP4623096A1/en
Publication of EP4623096A4 publication Critical patent/EP4623096A4/en
Pending legal-status Critical Current

Links

Classifications

    • 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
    • G16B20/10—Ploidy or copy number detection
    • 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
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • 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

Landscapes

  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Medical Informatics (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Zoology (AREA)
  • Evolutionary Biology (AREA)
  • Wood Science & Technology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP23895315.2A 2022-11-21 2023-11-20 Fragmentomics-based identification of tumor-specific copy number changes in liquid biopsy Pending EP4623096A4 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202263427058P 2022-11-21 2022-11-21
PCT/US2023/080494 WO2024112643A1 (en) 2022-11-21 2023-11-20 Fragmentomics based identification of tumor-specific copy number alteration states in liquid biopsy

Publications (2)

Publication Number Publication Date
EP4623096A1 EP4623096A1 (en) 2025-10-01
EP4623096A4 true EP4623096A4 (en) 2026-03-11

Family

ID=91196534

Family Applications (1)

Application Number Title Priority Date Filing Date
EP23895315.2A Pending EP4623096A4 (en) 2022-11-21 2023-11-20 Fragmentomics-based identification of tumor-specific copy number changes in liquid biopsy

Country Status (2)

Country Link
EP (1) EP4623096A4 (en)
WO (1) WO2024112643A1 (en)

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2018009723A1 (en) * 2016-07-06 2018-01-11 Guardant Health, Inc. Methods for fragmentome profiling of cell-free nucleic acids

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2019310041B2 (en) * 2018-07-23 2025-11-20 Guardant Health, Inc. Methods and systems for adjusting tumor mutational burden by tumor fraction and coverage
WO2022046947A1 (en) * 2020-08-25 2022-03-03 Guardant Health, Inc. Methods and systems for predicting an origin of a variant

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2018009723A1 (en) * 2016-07-06 2018-01-11 Guardant Health, Inc. Methods for fragmentome profiling of cell-free nucleic acids

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
CRISTIANO STEPHEN ET AL: "Genome-wide cell-free DNA fragmentation in patients with cancer", NATURE,, vol. 570, no. 7761, 29 May 2019 (2019-05-29), pages 385 - 389, XP036814426, [retrieved on 20190529], DOI: 10.1038/S41586-019-1272-6 *
See also references of WO2024112643A1 *

Also Published As

Publication number Publication date
EP4623096A1 (en) 2025-10-01
WO2024112643A1 (en) 2024-05-30

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