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

Systems and methods for evaluating tumor fraction Download PDF

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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
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Prior art keywords
tumor
sample
allele
fraction
coverage
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Pending
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CA3140066A
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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
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Foundation Medicine Inc
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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

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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
    • 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

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  • 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 (https=)
EP (1) EP3973530A4 (https=)
JP (1) JP7702360B2 (https=)
KR (1) KR20220011140A (https=)
CN (1) CN114026646A (https=)
AU (2) AU2020279752A1 (https=)
BR (1) BR112021022879A2 (https=)
CA (1) CA3140066A1 (https=)
IL (1) IL288182A (https=)
SG (1) SG11202111947PA (https=)
WO (1) WO2020236941A1 (https=)

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 (19)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ES3022582T3 (en) 2013-05-10 2025-05-28 Found Medicine Inc Analysis of genetic variants
JP2023552391A (ja) * 2020-12-03 2023-12-15 ファウンデーション・メディシン・インコーポレイテッド 治療を選択し、予想される治療転帰を判定するための木ベースのモデル
EP4266315A4 (en) * 2020-12-16 2024-11-20 Seedna Inc. METHOD FOR CALCULATING THE RELIABILITY VALUE OF A POLYMORPHISM LOCUS SIGNAL
WO2022271159A1 (en) * 2021-06-22 2022-12-29 Foundation Medicine, Inc. Systems and methods for evaluating tumor fraction
EP4374376A4 (en) * 2021-07-23 2025-05-28 Foundation Medicine, Inc. METHODS FOR DETERMINING VARIANT FREQUENCY AND MONITORING DISEASE PROGRESSION
JP2024538725A (ja) * 2021-10-08 2024-10-23 ファウンデーション・メディシン・インコーポレイテッド コピー数変化呼び出しに対する汚染を検出及び除去するための方法及びシステム
EP4430614A4 (en) * 2021-11-12 2025-12-17 Found Medicine Inc Circulating tumor DNA fraction and uses thereof
WO2023096658A1 (en) * 2021-11-23 2023-06-01 Foundation Medicine, Inc. Methods and systems for reporting clinically-actionable potential germline pathogenic variant sequences
US20250037823A1 (en) 2021-12-08 2025-01-30 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
CN119585730A (zh) * 2022-07-15 2025-03-07 基金会医学公司 用于确定患者样品中循环肿瘤dna分数的方法和系统
WO2024081859A2 (en) * 2022-10-14 2024-04-18 Foundation Medicine, Inc. Methods and systems for performing genomic variant calls based on identified off-target sequence reads
WO2024112967A1 (en) * 2022-11-27 2024-05-30 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
WO2025151838A1 (en) 2024-01-12 2025-07-17 Sana Biotechnology, Inc. Safety switches to control in vitro and in vivo proliferation of cell therapy products
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
CA2945962C (en) * 2014-04-21 2023-08-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
WO2015164432A1 (en) * 2014-04-21 2015-10-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
HUE058263T2 (hu) * 2015-02-10 2022-07-28 Univ Hong Kong Chinese Mutációk detektálása rákszûrési és magzatelemzési célból
BR112018005940A2 (pt) * 2015-09-25 2018-12-11 Contextual Genomics Inc métodos de garantia da qualidade molecular para uso em sequenciamento
CN114959918A (zh) * 2016-02-29 2022-08-30 基础医疗股份有限公司 用于评估肿瘤突变负荷的方法和系统
CA3067419A1 (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
JP7760242B2 (ja) * 2017-07-21 2025-10-27 ジェネンテック， インコーポレイテッド がんの治療法及び診断法

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

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