CN117561572A - 对同源修复缺陷进行分类的系统和方法 - Google Patents

对同源修复缺陷进行分类的系统和方法 Download PDF

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Publication number
CN117561572A
CN117561572A CN202280043825.4A CN202280043825A CN117561572A CN 117561572 A CN117561572 A CN 117561572A CN 202280043825 A CN202280043825 A CN 202280043825A CN 117561572 A CN117561572 A CN 117561572A
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hrd
feature
features
tumor
genome
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Chinese (zh)
Inventor
伊桑·索科尔
杰伊·摩尔
贾斯廷·纽伯格
戴斯特·金
陈奎廷
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Foundation Medical Co
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Foundation Medical Co
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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
    • 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
    • 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
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G06N20/20—Ensemble learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/08—Learning methods
    • G06N3/09—Supervised learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00—Computing arrangements using knowledge-based models
    • G06N5/01—Dynamic search techniques; Heuristics; Dynamic trees; Branch-and-bound
    • 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
    • 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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  • 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)
CN202280043825.4A 2021-06-25 2022-06-24 对同源修复缺陷进行分类的系统和方法 Pending CN117561572A (zh)

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
CN117561572A true CN117561572A (zh) 2024-02-13

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CN202280043825.4A Pending CN117561572A (zh) 2021-06-25 2022-06-24 对同源修复缺陷进行分类的系统和方法

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US (1) US20230140123A1 (enExample)
EP (1) EP4360094A4 (enExample)
JP (1) JP2024528489A (enExample)
CN (1) CN117561572A (enExample)
AU (1) AU2022299105A1 (enExample)
TW (1) TW202317774A (enExample)
WO (1) WO2022272310A1 (enExample)

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

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Publication number Publication date
AU2022299105A1 (en) 2024-01-04
EP4360094A4 (en) 2025-04-23
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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