CA3140066A1 - Systems and methods for evaluating tumor fraction - Google Patents

Systems and methods for evaluating tumor fraction Download PDF

Info

Publication number
CA3140066A1
CA3140066A1 CA3140066A CA3140066A CA3140066A1 CA 3140066 A1 CA3140066 A1 CA 3140066A1 CA 3140066 A CA3140066 A CA 3140066A CA 3140066 A CA3140066 A CA 3140066A CA 3140066 A1 CA3140066 A1 CA 3140066A1
Authority
CA
Canada
Prior art keywords
tumor
sample
allele
fraction
coverage
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
CA3140066A
Other languages
English (en)
French (fr)
Inventor
Bernard FENDLER
Jason D. HUGHES
Steven Roels
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 CA3140066A1 publication Critical patent/CA3140066A1/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
    • 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
    • C12Q1/6876—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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10—Ploidy or copy number 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
    • 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
    • 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
    • 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
    • C12Q2600/156—Polymorphic or mutational markers

Landscapes

  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Organic Chemistry (AREA)
  • Data Mining & Analysis (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Molecular Biology (AREA)
  • Pathology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Software Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Oncology (AREA)
  • General Engineering & Computer Science (AREA)
  • Hospice & Palliative Care (AREA)
  • Biomedical Technology (AREA)
  • Primary Health Care (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA3140066A 2019-05-20 2020-05-20 Systems and methods for evaluating tumor fraction Pending CA3140066A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201962850474P 2019-05-20 2019-05-20
US62/850,474 2019-05-20
PCT/US2020/033821 WO2020236941A1 (en) 2019-05-20 2020-05-20 Systems and methods for evaluating tumor fraction

Publications (1)

Publication Number Publication Date
CA3140066A1 true CA3140066A1 (en) 2020-11-26

Family

ID=73458622

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3140066A Pending CA3140066A1 (en) 2019-05-20 2020-05-20 Systems and methods for evaluating tumor fraction

Country Status (11)

Country Link
US (2) US20220243279A1 (enExample)
EP (1) EP3973530A4 (enExample)
JP (1) JP7702360B2 (enExample)
KR (1) KR20220011140A (enExample)
CN (1) CN114026646A (enExample)
AU (2) AU2020279752A1 (enExample)
BR (1) BR112021022879A2 (enExample)
CA (1) CA3140066A1 (enExample)
IL (1) IL288182A (enExample)
SG (1) SG11202111947PA (enExample)
WO (1) WO2020236941A1 (enExample)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4265739A4 (en) * 2021-03-02 2025-05-21 Peking University First Hospital GENE COMBINATION FOR HUMAN TUMOR PRIORITIZATION AND ITS USE

Families Citing this family (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2014262481A1 (en) 2013-05-10 2015-11-26 Foundation Medicine, Inc. Analysis of genetic variants
EP4256075A4 (en) * 2020-12-03 2024-10-23 Foundation Medicine, Inc. TREE MODEL FOR SELECTING TREATMENTS AND DETERMINING EXPECTED TREATMENT OUTCOMES
US20230227897A1 (en) * 2020-12-16 2023-07-20 Seedna Inc. Method for calculating the fidelity of the signal of polymorphic genetic loci
EP4359569A4 (en) * 2021-06-22 2025-02-26 Foundation Medicine, Inc. Systems and methods for evaluating tumor fraction
US20250095775A1 (en) * 2021-07-23 2025-03-20 Foundation Medicine, Inc. Methods for determining variant frequency and monitoring disease progression
CN118103916A (zh) * 2021-10-08 2024-05-28 基金会医学公司 用于检测和去除针对拷贝数改变调用的污染的方法和系统
EP4430614A4 (en) * 2021-11-12 2025-12-17 Found Medicine Inc Circulating tumor DNA fraction and uses thereof
EP4437122A4 (en) * 2021-11-23 2025-08-06 Found Medicine Inc METHODS AND SYSTEMS FOR REPORTING CLINICALLY ACTIVE POTENTIAL GERMLINE PATHOGENIC VARIANT SEQUENCES
WO2023107869A1 (en) 2021-12-08 2023-06-15 Foundation Medicine, Inc. Methods and systems for highlighting clinical information in diagnostic reports
CN114530200B (zh) * 2022-03-18 2022-09-23 北京阅微基因技术股份有限公司 基于计算snp熵值的混合样本鉴定方法
WO2024015973A1 (en) * 2022-07-15 2024-01-18 Foundation Medicine, Inc. Methods and systems for determining circulating tumor dna fraction in a patient sample
US20260141981A1 (en) * 2022-10-14 2026-05-21 Foundation Medicine, Inc. Methods and systems for performing genomic variant calls based on identified off-target sequence reads
US20260193351A1 (en) * 2022-11-27 2026-07-09 The University Of Chicago Methods for treating cancer with immunotherapy
EP4631049A4 (en) * 2022-12-09 2026-02-18 Found Medicine Inc METHODS AND SYSTEMS FOR DETERMINING THE CLONALITY OF SOMATIC SHORT VARIANTS
CN121219428A (zh) * 2023-05-15 2025-12-26 基金会医学公司 用于评定液体活检样品中循环肿瘤dna分数的方法和系统
WO2024238750A2 (en) * 2023-05-17 2024-11-21 Foundation Medicine, Inc. Clonal hematopoiesis burden as a biomarker for immune checkpoint inhibitor response
WO2025054202A1 (en) 2023-09-05 2025-03-13 Sana Biotechnology, Inc. Method of screening a sample comprising a transgene with a unique barcode
AU2025208175A1 (en) 2024-01-12 2026-06-25 Sana Biotechnology, Inc. Safety switches to control in vitro and in vivo proliferation of cell therapy products
WO2026102094A1 (en) * 2024-11-07 2026-05-15 Foundation Medicine, Inc. Combined chemistry and computational corrections for methyl-bias
WO2026165523A1 (en) 2025-01-31 2026-08-06 Foundation Medicine, Inc. Methods and systems for detecting howell-jolly bodies
CN121305088B (zh) * 2025-12-09 2026-03-17 中国人民解放军空军军医大学 迁移学习驱动的颅内肿瘤影像数据全自动分割方法

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20110301854A1 (en) * 2010-06-08 2011-12-08 Curry Bo U Method of Determining Allele-Specific Copy Number of a SNP
WO2014014498A1 (en) * 2012-07-20 2014-01-23 Verinata Health, Inc. Detecting and classifying copy number variation in a fetal genome
US11261494B2 (en) * 2012-06-21 2022-03-01 The Chinese University Of Hong Kong Method of measuring a fractional concentration of tumor DNA
RU2717641C2 (ru) * 2014-04-21 2020-03-24 Натера, Инк. Обнаружение мутаций и плоидности в хромосомных сегментах
WO2015164432A1 (en) * 2014-04-21 2015-10-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
DK3256605T3 (da) * 2015-02-10 2022-03-14 Univ Hong Kong Chinese Påvisning af mutationer til cancerscreening og føtal analyse
HK1255446A1 (zh) * 2015-09-25 2019-08-16 Canexia Health Inc. 分子质量保证方法在测序中的应用
WO2017151524A1 (en) * 2016-02-29 2017-09-08 Foundation Medicine, Inc. Methods and systems for evaluating tumor mutational burden
WO2018236911A1 (en) * 2017-06-20 2018-12-27 Illumina, Inc. Methods and systems for decomposition and quantification of dna mixtures from multiple contributors of known or unknown genotypes
AU2018304458B2 (en) * 2017-07-21 2021-12-09 Foundation Medicine, Inc. Therapeutic and diagnostic methods for cancer

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4265739A4 (en) * 2021-03-02 2025-05-21 Peking University First Hospital GENE COMBINATION FOR HUMAN TUMOR PRIORITIZATION AND ITS USE

Also Published As

Publication number Publication date
SG11202111947PA (en) 2021-12-30
BR112021022879A2 (pt) 2022-03-22
CN114026646A (zh) 2022-02-08
JP7702360B2 (ja) 2025-07-03
KR20220011140A (ko) 2022-01-27
EP3973530A4 (en) 2023-08-02
US20250259709A1 (en) 2025-08-14
JP2022533137A (ja) 2022-07-21
US20220243279A1 (en) 2022-08-04
EP3973530A1 (en) 2022-03-30
AU2025271452A1 (en) 2026-01-29
WO2020236941A1 (en) 2020-11-26
IL288182A (en) 2022-01-01
AU2020279752A1 (en) 2022-01-06

Similar Documents

Publication Publication Date Title
US20250259709A1 (en) Systems and methods for evaluating tumor fraction
JP7317078B2 (ja) 腫瘍変異負荷を評価するための方法及びシステム
US12473589B2 (en) Compositions and methods for evaluating genomic alterations
EP4359569A1 (en) Systems and methods for evaluating tumor fraction
EP4574996B1 (en) Detection and treatment of disease exhibiting disease cell heterogeneity and systems and methods for communicating test results
EP4427226A1 (en) System and method for identifying copy number alterations
HK40075645A (en) Method and system for assessing tumor mutation load
WO2024039998A9 (en) Methods and systems for detection of mismatch repair deficiency
EP4631049A1 (en) Methods and systems for determining clonality of somatic short variants
HK40002957B (en) Methods and systems for evaluating tumor mutational burden
HK40002957A (en) Methods and systems for evaluating tumor mutational burden

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20220923

B12 Application deemed to be withdrawn, abandoned or lapsed

Free format text: ST27 STATUS EVENT CODE: N-2-6-B10-B12-B303 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: DEEMED ABANDONED - FAILURE TO RESPOND TO AN EXAMINER'S REQUISITION

Effective date: 20240903

MFA Maintenance fee for application paid

Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 5TH ANNIV.) - STANDARD

Year of fee payment: 5

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: N-6-6-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20250425

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: N-6-6-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20250425

MFA Maintenance fee for application paid

Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 6TH ANNIV.) - STANDARD

Year of fee payment: 6

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: N-6-6-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20260409

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: N-6-6-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20260409