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)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Molecular Biology (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (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)
  • Pathology (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Public Health (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Epidemiology (AREA)
  • Computational Linguistics (AREA)
  • Oncology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biochemistry (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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Application Number Title Priority Date Filing Date
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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Country Link
US (1) US20230140123A1 (cg-RX-API-DMAC10.html)
EP (1) EP4360094A4 (cg-RX-API-DMAC10.html)
JP (1) JP2024528489A (cg-RX-API-DMAC10.html)
CN (1) CN117561572A (cg-RX-API-DMAC10.html)
AU (1) AU2022299105A1 (cg-RX-API-DMAC10.html)
TW (1) TW202317774A (cg-RX-API-DMAC10.html)
WO (1) WO2022272310A1 (cg-RX-API-DMAC10.html)

Families Citing this family (8)

* 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
US20260100247A1 (en) * 2022-09-30 2026-04-09 Foundation Medicine, Inc. Systems and methods for processing clinico-genomic data
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
EP4702163A1 (en) * 2023-04-28 2026-03-04 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

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20200255909A1 (en) * 2019-02-12 2020-08-13 Tempus Integrated machine-learning framework to estimate homologous recombination deficiency

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DK2981624T3 (da) * 2013-04-05 2020-03-02 Myriad Genetics Inc Fremgangsmåder til vurdering af homolog rekombinationsdeficiens og forudsigelse af respons på cancerbehandling
US11348661B2 (en) * 2018-05-14 2022-05-31 Tempus Labs, Inc. Predicting total nucleic acid yield and dissection boundaries for histology slides
WO2021119311A1 (en) * 2019-12-10 2021-06-17 Tempus Labs, Inc. Systems and methods for predicting homologous recombination deficiency status of a specimen

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20200255909A1 (en) * 2019-02-12 2020-08-13 Tempus Integrated machine-learning framework to estimate homologous recombination deficiency

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
LUAN NGUYEN等: "Pan-cancer landscape of homologous recombination deficiency", 《BIORXIV》, 19 June 2020 (2020-06-19), pages 12 - 17 *

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Publication number Publication date
US20230140123A1 (en) 2023-05-04
AU2022299105A1 (en) 2024-01-04
TW202317774A (zh) 2023-05-01
JP2024528489A (ja) 2024-07-30
EP4360094A4 (en) 2025-04-23
EP4360094A1 (en) 2024-05-01
WO2022272310A1 (en) 2022-12-29

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