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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  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Molecular Biology (AREA)
  • General Physics & Mathematics (AREA)
  • Mathematical Physics (AREA)
  • Computational Mathematics (AREA)
  • Pure & Applied Mathematics (AREA)
  • Mathematical Optimization (AREA)
  • Mathematical Analysis (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Data Mining & Analysis (AREA)
  • Computing Systems (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Animal Behavior & Ethology (AREA)
  • Medicinal Chemistry (AREA)
  • Physiology (AREA)
  • Library & Information Science (AREA)
  • Biochemistry (AREA)
  • Databases & Information Systems (AREA)
  • Algebra (AREA)
  • Operations Research (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

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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 (https=)
EP (1) EP3210141A1 (https=)
JP (1) JP6707081B2 (https=)
AU (1) AU2015336005B2 (https=)
CA (1) CA2965163A1 (https=)
WO (1) WO2016064995A1 (https=)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2015336005B2 (en) 2014-10-22 2018-07-26 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
CA3014292A1 (en) 2016-02-12 2017-08-17 Regeneron Pharmaceuticals, Inc. Methods and systems for detection of abnormal karyotypes
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
CN116584267A (zh) * 2022-08-01 2023-08-15 中国农业科学院都市农业研究所 一种促进植物地上部或地下部生长的光源排列方法

Family Cites Families (5)

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Publication number Priority date Publication date Assignee Title
JP2003508853A (ja) * 1999-08-27 2003-03-04 アイリス・バイオ・テクノロジーズ・インコーポレイテッド 遺伝子分析用人工知能システム
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
AU2015336005B2 (en) 2014-10-22 2018-07-26 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
AU2015336005A1 (en) 2017-05-11
US10886005B2 (en) 2021-01-05
EP3210141A1 (en) 2017-08-30
CA2965163A1 (en) 2016-04-28
JP2017537380A (ja) 2017-12-14
WO2016064995A1 (en) 2016-04-28
JP6707081B2 (ja) 2020-06-10
US20170316148A1 (en) 2017-11-02

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