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WO2016018481A3 - Network based stratification of tumor mutations - Google Patents

Network based stratification of tumor mutations Download PDF

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Publication number
WO2016018481A3
WO2016018481A3 PCT/US2015/028343 US2015028343W WO2016018481A3 WO 2016018481 A3 WO2016018481 A3 WO 2016018481A3 US 2015028343 W US2015028343 W US 2015028343W WO 2016018481 A3 WO2016018481 A3 WO 2016018481A3
Authority
WO
WIPO (PCT)
Prior art keywords
network based
tumor mutations
based stratification
stratification
subject
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2015/028343
Other languages
French (fr)
Other versions
WO2016018481A2 (en
Inventor
Trey Ideker
Matan HOFREE
John Paul Shen
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.)
University of California Berkeley
University of California San Diego UCSD
Original Assignee
University of California Berkeley
University of California San Diego UCSD
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by University of California Berkeley, University of California San Diego UCSD filed Critical University of California Berkeley
Publication of WO2016018481A2 publication Critical patent/WO2016018481A2/en
Publication of WO2016018481A3 publication Critical patent/WO2016018481A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • 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
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • 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
    • 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
    • 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
    • C12Q2600/154—Methylation markers
    • 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
    • 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
    • C12Q2600/158—Expression markers
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Analytical Chemistry (AREA)
  • Databases & Information Systems (AREA)
  • Organic Chemistry (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Software Systems (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Oncology (AREA)
  • Microbiology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

The embodiments provide a method of for stratification of cancer into one or more informative subtypes of a subject in need thereof. The embodiments, further provide assigning a subject in need into one or more informative subtypes, including assigning a subject in need into an informative subtype wherein the subtype is an ovarian cancer subtype.
PCT/US2015/028343 2014-07-28 2015-04-29 Network based stratification of tumor mutations Ceased WO2016018481A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201462029868P 2014-07-28 2014-07-28
US62/029,868 2014-07-28

Publications (2)

Publication Number Publication Date
WO2016018481A2 WO2016018481A2 (en) 2016-02-04
WO2016018481A3 true WO2016018481A3 (en) 2016-03-03

Family

ID=55218434

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2015/028343 Ceased WO2016018481A2 (en) 2014-07-28 2015-04-29 Network based stratification of tumor mutations

Country Status (1)

Country Link
WO (1) WO2016018481A2 (en)

Families Citing this family (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR102500659B1 (en) 2016-02-29 2023-02-16 제넨테크, 인크. Therapeutic and diagnostic methods for cancer
US11725247B2 (en) 2016-02-29 2023-08-15 Foundation Medicine, Inc. Methods of treating cancer
KR102358206B1 (en) * 2016-02-29 2022-02-04 파운데이션 메디신 인코포레이티드 Methods and systems for assessing tumor mutational burden
WO2017220782A1 (en) * 2016-06-24 2017-12-28 Molecular Health Gmbh Screening method for endometrial cancer
KR102804118B1 (en) 2016-10-06 2025-05-09 제넨테크, 인크. Treatment and Diagnosis of Cancer
EP3535422A2 (en) * 2016-11-07 2019-09-11 Grail, Inc. Methods of identifying somatic mutational signatures for early cancer detection
KR20200013731A (en) * 2017-06-01 2020-02-07 난토믹스, 엘엘씨 INVESTIGATING TUMORAL AND TEMPORAL HETEROGENEITY THROUGH COMPREHENSIVE -OMICS PROFILING IN PATIENTS WITH METASTATIC TRIPLE NEGATIVE BREAST CANCER
US11674962B2 (en) 2017-07-21 2023-06-13 Genentech, Inc. Therapeutic and diagnostic methods for cancer
CA3083792A1 (en) 2017-12-18 2019-06-27 Personal Genome Diagnostics Inc. Machine learning system and method for somatic mutation discovery
US11887698B2 (en) * 2020-01-08 2024-01-30 Samsung Electronics Co., Ltd. Method and electronic device for building comprehensive genome scale metabolic model
CN117677714A (en) * 2021-05-19 2024-03-08 特拉维夫大学拉莫特有限公司 Cancer classification and prognosis based on silent and nonsilent mutations
CN113736790B (en) * 2021-10-14 2023-05-02 四川农业大学 sgRNA (ribonucleic acid) for knocking out duck hnRNPA3 gene, cell line, construction method and application thereof
EP4490731A1 (en) * 2022-03-10 2025-01-15 Lantern Pharma Inc. Computerized systems and methods for ensemble model-based drug discovery
CN114972163B (en) * 2022-03-15 2025-02-18 常州桐树生物科技有限公司 A method for identifying microsatellite instability states based on graph convolutional neural network
CN115966316B (en) * 2023-02-10 2023-07-04 北京大学 Tumor drug sensitivity prediction method, system, equipment and storage medium
WO2025178968A2 (en) * 2024-02-21 2025-08-28 The Regents Of The University Of California Non-coding functional variants as cancer biomarkers

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
AVESSON ET AL.: "The emerging role of RNA and DNA editing in cancer", BIOCHEM BIOPHYS ACTA, vol. 1845, no. 2, pages 308 - 316 *
DATABASE GenBank [o] 14 November 2006 (2006-11-14), "Homo sapiens partial TTN gene for titin", Database accession no. AJ277892.2 *
DATABASE UNIPROT [o] 9 July 2014 (2014-07-09), "Titin human.", Database accession no. Q8WZ42. *
GREENMAN ET AL.: "Patterns of somatic mutation in human cancer genomes.", NATURE, vol. 446, no. 7132, 8 March 2007 (2007-03-08), pages 153 - 158, XP055155126, DOI: doi:10.1038/nature05610 *
HOFREE ET AL.: "Network-based stratification of tumor mutations.", NATURE METHODS, vol. 10, no. 11, 5 September 2013 (2013-09-05), pages 1108 - 1115, XP055193269, DOI: doi:10.1038/nmeth.2651 *
KARVE ET AL.: "Small changes huge impact: the role of protein posttranslational modifications in cellular homeostasis and disease", J AMINO ACIDS, vol. 2011, no. 207691, pages 1 - 13 *

Also Published As

Publication number Publication date
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