AU2015336005B2 - Method to identify genes under positive selection - Google Patents

Method to identify genes under positive selection Download PDF

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Publication number
AU2015336005B2
AU2015336005B2 AU2015336005A AU2015336005A AU2015336005B2 AU 2015336005 B2 AU2015336005 B2 AU 2015336005B2 AU 2015336005 A AU2015336005 A AU 2015336005A AU 2015336005 A AU2015336005 A AU 2015336005A AU 2015336005 B2 AU2015336005 B2 AU 2015336005B2
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mutations
scores
distributions
genes
evolutionary
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AU2015336005A
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AU2015336005A1 (en
Inventor
Teng-Kuei Hsu
Panagiotis KATSONIS
Amanda Michele Koire
Olivier Lichtarge
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Baylor College of Medicine
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Baylor College of Medicine
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    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/11—Complex mathematical operations for solving equations, e.g. nonlinear equations, general mathematical optimization problems
    • G06F17/13—Differential equations
    • 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
    • G16B10/00—ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
    • 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
    • G16B35/00—ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/60—In silico combinatorial chemistry
    • 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
    • G16B20/40—Population genetics; Linkage disequilibrium

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  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Molecular Biology (AREA)
  • Mathematical Physics (AREA)
  • General Physics & Mathematics (AREA)
  • Computational Mathematics (AREA)
  • Pure & Applied Mathematics (AREA)
  • Mathematical Optimization (AREA)
  • Mathematical Analysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Data Mining & Analysis (AREA)
  • Biochemistry (AREA)
  • Physiology (AREA)
  • Computing Systems (AREA)
  • Animal Behavior & Ethology (AREA)
  • Library & Information Science (AREA)
  • Medicinal Chemistry (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Algebra (AREA)
  • Operations Research (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
AU2015336005A 2014-10-22 2015-10-21 Method to identify genes under positive selection Ceased AU2015336005B2 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201462067294P 2014-10-22 2014-10-22
US62/067,294 2014-10-22
PCT/US2015/056646 WO2016064995A1 (en) 2014-10-22 2015-10-21 Method to identify genes under positive selection

Publications (2)

Publication Number Publication Date
AU2015336005A1 AU2015336005A1 (en) 2017-05-11
AU2015336005B2 true AU2015336005B2 (en) 2018-07-26

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
AU2015336005A Ceased AU2015336005B2 (en) 2014-10-22 2015-10-21 Method to identify genes under positive selection

Country Status (6)

Country Link
US (1) US10886005B2 (enExample)
EP (1) EP3210141A1 (enExample)
JP (1) JP6707081B2 (enExample)
AU (1) AU2015336005B2 (enExample)
CA (1) CA2965163A1 (enExample)
WO (1) WO2016064995A1 (enExample)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2965163A1 (en) 2014-10-22 2016-04-28 Baylor College Of Medicine Method to identify genes under positive selection
US10395759B2 (en) 2015-05-18 2019-08-27 Regeneron Pharmaceuticals, Inc. Methods and systems for copy number variant detection
CN109074426B (zh) 2016-02-12 2022-07-26 瑞泽恩制药公司 用于检测异常核型的方法和系统
US11281977B2 (en) * 2017-07-31 2022-03-22 Cognizant Technology Solutions U.S. Corporation Training and control system for evolving solutions to data-intensive problems using epigenetic enabled individuals
CN110782947A (zh) * 2019-10-18 2020-02-11 湖南大学 基于蛋白质序列功能区域的癌症驱动识别
WO2021178952A1 (en) * 2020-03-06 2021-09-10 The Research Institute At Nationwide Children's Hospital Genome dashboard
CN113643754B (zh) * 2021-08-11 2023-12-29 苏州赛美科基因科技有限公司 一种错义变异基因的评分处理方法、优化评分方法及装置

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001016860A2 (en) * 1999-08-27 2001-03-08 Iris Bio Technologies, Inc. Artificial intelligence system for genetic analysis
US20040023296A1 (en) 2001-11-28 2004-02-05 Baylor College Of Medicine Use of quantitative evolutionary trace analysis to determine functional residues
KR101325736B1 (ko) 2010-10-27 2013-11-08 삼성에스디에스 주식회사 바이오 마커 추출 장치 및 방법
WO2014007865A1 (en) 2012-07-03 2014-01-09 Baylor College Of Medicine Evolutionary-gradient scoring of tp53 mutations (egsp53) defines risk in resectable head and neck cancer
CA2965163A1 (en) 2014-10-22 2016-04-28 Baylor College Of Medicine Method to identify genes under positive selection

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
KATSONIS, P. et al "A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness" GENOME RESEARCH, vol. 24, no. 12 published 12 Sept 2014, pages 2050-2058 *

Also Published As

Publication number Publication date
EP3210141A1 (en) 2017-08-30
WO2016064995A1 (en) 2016-04-28
US20170316148A1 (en) 2017-11-02
CA2965163A1 (en) 2016-04-28
JP2017537380A (ja) 2017-12-14
JP6707081B2 (ja) 2020-06-10
AU2015336005A1 (en) 2017-05-11
US10886005B2 (en) 2021-01-05

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