AU2020279752A1 - Systems and methods for evaluating tumor fraction - Google Patents

Systems and methods for evaluating tumor fraction Download PDF

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Publication number
AU2020279752A1
AU2020279752A1 AU2020279752A AU2020279752A AU2020279752A1 AU 2020279752 A1 AU2020279752 A1 AU 2020279752A1 AU 2020279752 A AU2020279752 A AU 2020279752A AU 2020279752 A AU2020279752 A AU 2020279752A AU 2020279752 A1 AU2020279752 A1 AU 2020279752A1
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AU
Australia
Prior art keywords
tumor
sample
allele
fraction
coverage
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Abandoned
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AU2020279752A
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English (en)
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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Filing date
Publication date
Application filed by Foundation Medicine Inc filed Critical Foundation Medicine Inc
Publication of AU2020279752A1 publication Critical patent/AU2020279752A1/en
Priority to AU2025271452A priority Critical patent/AU2025271452A1/en
Abandoned 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)
AU2020279752A 2019-05-20 2020-05-20 Systems and methods for evaluating tumor fraction Abandoned AU2020279752A1 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2025271452A AU2025271452A1 (en) 2019-05-20 2025-11-27 Systems and methods for evaluating tumor fraction

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

Related Child Applications (1)

Application Number Title Priority Date Filing Date
AU2025271452A Division AU2025271452A1 (en) 2019-05-20 2025-11-27 Systems and methods for evaluating tumor fraction

Publications (1)

Publication Number Publication Date
AU2020279752A1 true AU2020279752A1 (en) 2022-01-06

Family

ID=73458622

Family Applications (2)

Application Number Title Priority Date Filing Date
AU2020279752A Abandoned AU2020279752A1 (en) 2019-05-20 2020-05-20 Systems and methods for evaluating tumor fraction
AU2025271452A Pending AU2025271452A1 (en) 2019-05-20 2025-11-27 Systems and methods for evaluating tumor fraction

Family Applications After (1)

Application Number Title Priority Date Filing Date
AU2025271452A Pending AU2025271452A1 (en) 2019-05-20 2025-11-27 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)

Families Citing this family (22)

* 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
CN113025716A (zh) * 2021-03-02 2021-06-25 北京大学第一医院 一种用于人肿瘤分级的基因组合及其用途
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

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
CA3140066A1 (en) 2020-11-26
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

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