CA3246524A1 - TUMOR PRESENCE DETECTION BASED ON THE METHYLATION STATE OF ACELLULAR NUCLEIC ACID MOLECULES - Google Patents

TUMOR PRESENCE DETECTION BASED ON THE METHYLATION STATE OF ACELLULAR NUCLEIC ACID MOLECULES

Info

Publication number
CA3246524A1
CA3246524A1 CA3246524A CA3246524A CA3246524A1 CA 3246524 A1 CA3246524 A1 CA 3246524A1 CA 3246524 A CA3246524 A CA 3246524A CA 3246524 A CA3246524 A CA 3246524A CA 3246524 A1 CA3246524 A1 CA 3246524A1
Authority
CA
Canada
Prior art keywords
individual
regions
additional
computing system
cancer
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
CA3246524A
Other languages
English (en)
French (fr)
Inventor
Yupeng He
Zhaoren HE
Ariel JAIMOVICH
William Walter YOUNG GREENWALD
William J. Greenleaf
Sai Chen
Tingting Jiang
Jun Zhao
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 CA3246524A1 publication Critical patent/CA3246524A1/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
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] 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
    • C12Q1/6876—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
    • 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
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/40—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
    • G16H20/10—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to drugs or medications, e.g. for ensuring correct administration to patients
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
    • G16H20/40—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to mechanical, radiation or invasive therapies, e.g. surgery, laser therapy, dialysis or acupuncture
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/70—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
    • 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

  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Medical Informatics (AREA)
  • Public Health (AREA)
  • General Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Epidemiology (AREA)
  • Chemical & Material Sciences (AREA)
  • Primary Health Care (AREA)
  • Data Mining & Analysis (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Pathology (AREA)
  • Biomedical Technology (AREA)
  • Databases & Information Systems (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Software Systems (AREA)
  • Surgery (AREA)
  • Evolutionary Computation (AREA)
  • Oncology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Urology & Nephrology (AREA)
  • Hospice & Palliative Care (AREA)
  • Medicinal Chemistry (AREA)
CA3246524A 2022-04-07 2023-04-07 TUMOR PRESENCE DETECTION BASED ON THE METHYLATION STATE OF ACELLULAR NUCLEIC ACID MOLECULES Pending CA3246524A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202263328602P 2022-04-07 2022-04-07
US63/328,602 2022-04-07
US202263336852P 2022-04-29 2022-04-29
US63/336,852 2022-04-29
PCT/US2023/065560 WO2023197004A1 (en) 2022-04-07 2023-04-07 Detecting the presence of a tumor based on methylation status of cell-free nucleic acid molecules

Publications (1)

Publication Number Publication Date
CA3246524A1 true CA3246524A1 (en) 2023-10-12

Family

ID=86328669

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3246524A Pending CA3246524A1 (en) 2022-04-07 2023-04-07 TUMOR PRESENCE DETECTION BASED ON THE METHYLATION STATE OF ACELLULAR NUCLEIC ACID MOLECULES

Country Status (5)

Country Link
US (1) US20250273295A1 (https=)
EP (1) EP4504971A1 (https=)
JP (1) JP2025513786A (https=)
CA (1) CA3246524A1 (https=)
WO (1) WO2023197004A1 (https=)

Families Citing this family (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115457361A (zh) * 2022-09-19 2022-12-09 京东方科技集团股份有限公司 分类模型获取方法、表达类别确定方法、装置、设备及介质
US20250125050A1 (en) * 2023-10-13 2025-04-17 Tempus Ai, Inc. Systems and methods for molecular residual disease liquid biopsy assay
GB202317261D0 (en) * 2023-11-10 2023-12-27 Cancer Research Tech Ltd Methods for determining cancers
WO2025106275A1 (en) * 2023-11-15 2025-05-22 Guardant Health, Inc. Minimum residual disease (mrd) detection in early stage cancer using urine
WO2025155784A1 (en) * 2024-01-18 2025-07-24 Grail, Inc. Systems and methods to identify clonal hematopoiesis related methylation signatures
WO2026076332A1 (en) * 2024-10-03 2026-04-09 Guardant Health, Inc. Methods involving multi-modal tumor variant identification and tracking of tumor molecules

Family Cites Families (17)

* 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
WO2003046146A2 (en) 2001-11-28 2003-06-05 Applera Corporation Compositions and methods of selective nucleic acid isolation
ATE443765T1 (de) 2003-03-21 2009-10-15 Santaris Pharma As Analoga kurzer interferierender rna (sirna)
US20110028333A1 (en) * 2009-05-01 2011-02-03 Brown University Diagnosing, prognosing, and early detection of cancers by dna methylation profiling
US8835358B2 (en) 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
GB2559073A (en) 2012-06-08 2018-07-25 Pacific Biosciences California Inc Modified base detection with nanopore sequencing
CN104781421B (zh) 2012-09-04 2020-06-05 夸登特健康公司 检测稀有突变和拷贝数变异的系统和方法
EP4358097A1 (en) 2014-07-25 2024-04-24 University of Washington Methods of determining tissues and/or cell types giving rise to cell-free dna, and methods of identifying a disease or disorder using same
WO2018009723A1 (en) 2016-07-06 2018-01-11 Guardant Health, Inc. Methods for fragmentome profiling of cell-free nucleic acids
US9850523B1 (en) 2016-09-30 2017-12-26 Guardant Health, Inc. Methods for multi-resolution analysis of cell-free nucleic acids
MX2019007444A (es) 2016-12-22 2019-08-16 Guardant Health Inc Metodos y sistemas para analisis de moleculas de acido nucleico.
WO2020160414A1 (en) 2019-01-31 2020-08-06 Guardant Health, Inc. Compositions and methods for isolating cell-free dna
ES2994567T3 (en) * 2019-02-05 2025-01-27 Grail Inc Detecting cancer, cancer tissue of origin, and/or a cancer cell type
US20210407623A1 (en) * 2020-03-31 2021-12-30 Guardant Health, Inc. Determining tumor fraction for a sample based on methyl binding domain calibration data
EP4153771A4 (en) 2020-05-19 2024-07-24 The Trustees of the University of Pennsylvania COMPOSITIONS AND METHODS FOR CARBOXYMETHYLATION OF DNA CYTOSINE
CA3225385A1 (en) 2021-07-12 2023-01-19 The Trustees Of The University Of Pennsylvania Modified adapters for enzymatic dna deamination and methods of use thereof for epigenetic sequencing of free and immobilized dna

Also Published As

Publication number Publication date
JP2025513786A (ja) 2025-04-30
EP4504971A1 (en) 2025-02-12
US20250273295A1 (en) 2025-08-28
WO2023197004A1 (en) 2023-10-12

Similar Documents

Publication Publication Date Title
US12421559B2 (en) Identification and use of circulating nucleic acid tumor markers
US20250273295A1 (en) Detecting the presence of a tumor based on methylation status of cell-free nucleic acid molecules
US11965215B2 (en) Methods and systems for analyzing nucleic acid molecules
US20210340631A1 (en) Methods for subtyping of lung squamous cell carcinoma
EP4567125A2 (en) Systems and methods for sample preparation, sample sequencing, and sequencing data bias correction and quality control
EP4189111B1 (en) Methods for isolating cell-free dna
US11783912B2 (en) Methods and systems for analyzing nucleic acid molecules
US20260009072A1 (en) Methods and compositions for quantifying immune cell dna
EP4718460A2 (en) Methods and systems for analyzing nucleic acid molecules
US20240344115A1 (en) Methods and compositions for quantifying immune cell dna
US20220136070A1 (en) Methods and systems for characterizing tumor response to immunotherapy using an immunogenic profile
JP2025076406A (ja) がん免疫療法に対する応答を予測するための方法、システム及び組成物
HK40121346A (en) Methods and systems for analyzing nucleic acid molecules
엄혜현 Analysis of genetic heterogeneity of tumor-infiltrating immune cells in human cancer by single-cell RNA sequencing

Legal Events

Date Code Title Description
A00 Application filed

Free format text: ST27 STATUS EVENT CODE: A-0-1-A10-A00-A101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: APPLICATION RECEIVED - PCT

Effective date: 20240923

A00 Application filed

Free format text: ST27 STATUS EVENT CODE: A-1-1-A10-A00-A102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: COMPLIANCE REQUIREMENTS DETERMINED MET

Effective date: 20241001

A15 Pct application entered into the national or regional phase

Free format text: ST27 STATUS EVENT CODE: A-1-1-A10-A15-X000 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: NATIONAL ENTRY REQUIREMENTS DETERMINED COMPLIANT

Effective date: 20241001

P18 Priority claim added or amended

Free format text: ST27 STATUS EVENT CODE: A-1-1-P10-P18-P105 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: PRIORITY CLAIM REQUIREMENTS DETERMINED COMPLIANT

Effective date: 20241001

W00 Other event occurred

Free format text: ST27 STATUS EVENT CODE: A-1-1-W10-W00-W100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: LETTER SENT

Effective date: 20250213

MFA Maintenance fee for application paid

Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 2ND ANNIV.) - STANDARD

Year of fee payment: 2

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-1-1-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20250328

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-1-1-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20250328