AU2022299105A1 - System and method of classifying homologous repair deficiency - Google Patents

System and method of classifying homologous repair deficiency Download PDF

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Publication number
AU2022299105A1
AU2022299105A1 AU2022299105A AU2022299105A AU2022299105A1 AU 2022299105 A1 AU2022299105 A1 AU 2022299105A1 AU 2022299105 A AU2022299105 A AU 2022299105A AU 2022299105 A AU2022299105 A AU 2022299105A AU 2022299105 A1 AU2022299105 A1 AU 2022299105A1
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classifying
repair deficiency
homologous repair
homologous
deficiency
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AU2022299105A
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Kuei-Ting Chen
Dexter JIN
Jay Moore
Justin NEWBERG
Ethan Sokol
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Foundation Medicine Inc
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Foundation Medicine Inc
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    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10Ploidy or copy number detection
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00Machine learning
    • G06N20/20Ensemble learning
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/02Neural networks
    • G06N3/08Learning methods
    • G06N3/09Supervised learning
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00Computing arrangements using knowledge-based models
    • G06N5/01Dynamic search techniques; Heuristics; Dynamic trees; Branch-and-bound
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20Supervised data analysis
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers

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  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • Data Mining & Analysis (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Molecular Biology (AREA)
  • Software Systems (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • General Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Mathematical Physics (AREA)
  • General Physics & Mathematics (AREA)
  • Computing Systems (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Zoology (AREA)
  • Pathology (AREA)
  • Public Health (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Computational Linguistics (AREA)
  • Biochemistry (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
AU2022299105A 2021-06-25 2022-06-24 System and method of classifying homologous repair deficiency Pending AU2022299105A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202163215281P 2021-06-25 2021-06-25
US63/215,281 2021-06-25
PCT/US2022/073167 WO2022272310A1 (en) 2021-06-25 2022-06-24 System and method of classifying homologous repair deficiency

Publications (1)

Publication Number Publication Date
AU2022299105A1 true AU2022299105A1 (en) 2024-01-04

Family

ID=84545873

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2022299105A Pending AU2022299105A1 (en) 2021-06-25 2022-06-24 System and method of classifying homologous repair deficiency

Country Status (7)

Country Link
US (1) US20230140123A1 (https=)
EP (1) EP4360094A4 (https=)
JP (1) JP2024528489A (https=)
CN (1) CN117561572A (https=)
AU (1) AU2022299105A1 (https=)
TW (1) TW202317774A (https=)
WO (1) WO2022272310A1 (https=)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20260080973A1 (en) * 2022-08-30 2026-03-19 Foundation Medicine, Inc. Systems and methods for classifying and treating homologous repair deficiency cancers
WO2024077041A2 (en) * 2022-10-05 2024-04-11 Foundation Medicine, Inc. Methods and systems for identifying copy number signatures
CN116451070B (zh) * 2023-03-17 2025-12-19 南京康尼机电股份有限公司 基于多分辨率窗口的轨道车门系统异常判别方法及系统
AU2024264089A1 (en) * 2023-04-28 2025-10-02 Institut Curie Methods for diagnosing a homologous recombination deficiency in human tumors
CN116312781B (zh) * 2023-05-17 2023-08-18 普瑞基准科技(北京)有限公司 一种基于机器学习的基因组不稳定性评估方法及系统
CN117011615B (zh) * 2023-09-15 2025-12-19 湖南自兴智慧医疗科技有限公司 基于生成式模型数据增广的微核血细胞识别系统
WO2025217185A1 (en) * 2024-04-09 2025-10-16 Foundation Medicine, Inc. Parp inhibitors for the treatment of advanced prostate cancer

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2014248007B2 (en) * 2013-04-05 2020-03-26 Myriad Genetics, Inc. Methods and materials for assessing homologous recombination deficiency
US11348661B2 (en) * 2018-05-14 2022-05-31 Tempus Labs, Inc. Predicting total nucleic acid yield and dissection boundaries for histology slides
US10975445B2 (en) * 2019-02-12 2021-04-13 Tempus Labs, Inc. Integrated machine-learning framework to estimate homologous recombination deficiency
ES2989374T3 (es) * 2019-12-10 2024-11-26 Tempus Ai Inc Sistemas y procedimientos para predecir el estado de deficiencia de recombinación homóloga de una muestra

Also Published As

Publication number Publication date
EP4360094A4 (en) 2025-04-23
CN117561572A (zh) 2024-02-13
EP4360094A1 (en) 2024-05-01
JP2024528489A (ja) 2024-07-30
US20230140123A1 (en) 2023-05-04
TW202317774A (zh) 2023-05-01
WO2022272310A1 (en) 2022-12-29

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