WO2002035442A3 - Composite haplotype counts for multiple loci and alleles and association tests with continuous or discrete phenotypes - Google Patents

Composite haplotype counts for multiple loci and alleles and association tests with continuous or discrete phenotypes Download PDF

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Publication number
WO2002035442A3
WO2002035442A3 PCT/US2001/045393 US0145393W WO0235442A3 WO 2002035442 A3 WO2002035442 A3 WO 2002035442A3 US 0145393 W US0145393 W US 0145393W WO 0235442 A3 WO0235442 A3 WO 0235442A3
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WO
WIPO (PCT)
Prior art keywords
alleles
markers
continuous
multiple loci
subset
Prior art date
Application number
PCT/US2001/045393
Other languages
French (fr)
Other versions
WO2002035442A2 (en
Inventor
Dmitri Zaykin
Original Assignee
Glaxo Group Ltd
Dmitri Zaykin
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 Glaxo Group Ltd, Dmitri Zaykin filed Critical Glaxo Group Ltd
Priority to EP01988909A priority Critical patent/EP1350212A2/en
Priority to AU2002227113A priority patent/AU2002227113A1/en
Publication of WO2002035442A2 publication Critical patent/WO2002035442A2/en
Publication of WO2002035442A3 publication Critical patent/WO2002035442A3/en

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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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • G16B20/40—Population genetics; Linkage disequilibrium
    • 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

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Chemical & Material Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Ecology (AREA)
  • Physiology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Haplotype frequencies for a plurality of individuals are associated with a continuous trait. Each individual includes a pair of chromosomes having a plurality of markers thereon. Each marker has a pair of alleles for an individual. A haplotype includes a combination of alleles for a set of markers on a predetermined chromosome. A subset of markers from the set of markers that may correlate with the continuous trait, is selected. A value of the continuous trait, and a pair of alleles for each of the markers in the subset of markers, is obtained for each individual. For each individual, probabilities of haplotypes that are compatible with the alleles in the subset of markers is determined. Finally, a regression is performed on the probabilities of haplotypes that are compatible with the alleles in the subset of markers, for all the individuals, to determine correlation between the continuous trait and the haplotypes.
PCT/US2001/045393 2000-10-23 2001-10-22 Composite haplotype counts for multiple loci and alleles and association tests with continuous or discrete phenotypes WO2002035442A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP01988909A EP1350212A2 (en) 2000-10-23 2001-10-22 Composite haplotype counts for multiple loci and alleles and association tests with continuous or discrete phenotypes
AU2002227113A AU2002227113A1 (en) 2000-10-23 2001-10-22 Composite haplotype counts for multiple loci and alleles and association tests with continuous or discrete phenotypes

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US69474800A 2000-10-23 2000-10-23
US09/694,748 2000-10-23
US28878901P 2001-04-13 2001-04-13
US60/288,789 2001-04-13
US32734801P 2001-10-04 2001-10-04
US60/327,348 2001-10-04

Publications (2)

Publication Number Publication Date
WO2002035442A2 WO2002035442A2 (en) 2002-05-02
WO2002035442A3 true WO2002035442A3 (en) 2003-07-31

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/045393 WO2002035442A2 (en) 2000-10-23 2001-10-22 Composite haplotype counts for multiple loci and alleles and association tests with continuous or discrete phenotypes

Country Status (2)

Country Link
EP (1) EP1350212A2 (en)
WO (1) WO2002035442A2 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
FI114551B (en) * 2001-06-13 2004-11-15 Licentia Oy Computer-readable memory means and computer system for gene localization from chromosome and phenotype data
US7107155B2 (en) 2001-12-03 2006-09-12 Dnaprint Genomics, Inc. Methods for the identification of genetic features for complex genetics classifiers
EP2929070A4 (en) 2012-12-05 2016-06-01 Genepeeks Inc System and method for the computational prediction of expression of single-gene phenotypes

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999054500A2 (en) * 1998-04-21 1999-10-28 Genset Biallelic markers for use in constructing a high density disequilibrium map of the human genome
EP0955382A2 (en) * 1998-05-07 1999-11-10 Affymetrix, Inc. (a California Corporation) Polymorphisms associated with hypertension
WO2000051053A1 (en) * 1999-02-26 2000-08-31 Gemini Genomics (Uk) Limited Clinical and diagnostic database
WO2001091026A2 (en) * 2000-05-25 2001-11-29 Genset S.A. Methods of dna marker-based genetic analysis using estimated haplotype frequencies and uses thereof
WO2002020835A2 (en) * 2000-09-04 2002-03-14 Glaxo Group Limited Genetic study

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999054500A2 (en) * 1998-04-21 1999-10-28 Genset Biallelic markers for use in constructing a high density disequilibrium map of the human genome
EP0955382A2 (en) * 1998-05-07 1999-11-10 Affymetrix, Inc. (a California Corporation) Polymorphisms associated with hypertension
WO2000051053A1 (en) * 1999-02-26 2000-08-31 Gemini Genomics (Uk) Limited Clinical and diagnostic database
WO2001091026A2 (en) * 2000-05-25 2001-11-29 Genset S.A. Methods of dna marker-based genetic analysis using estimated haplotype frequencies and uses thereof
WO2002020835A2 (en) * 2000-09-04 2002-03-14 Glaxo Group Limited Genetic study

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DORUM A ET AL: "A BRCA1 founder mutation, identified with haplotype analysis, allowing genotype/phenotype determination and predictive testing", EUROPEAN JOURNAL OF CANCER, PERGAMON PRESS, OXFORD, GB, vol. 33, no. 14, December 1997 (1997-12-01), pages 2390 - 2392, XP004284601, ISSN: 0959-8049 *
FALLIN D ET AL: "Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data", AMERICAN JOURNAL OF HUMAN GENETICS, AMERICAN SOCIETY OF HUMAN GENETICS, CHICAGO, IL, US, vol. 67, no. 4, 1 October 2000 (2000-10-01), pages 947 - 959, XP002210146, ISSN: 0002-9297 *
LONG J C ET AL: "AN E-M ALGORITHM AND TESTING STRATEGY FOR MULTIPLE-LOCUS HAPLOTYPES", AMERICAN JOURNAL OF HUMAN GENETICS, UNIVERSITY OF CHICAGO PRESS, CHICAGO,, US, vol. 56, 1995, pages 799 - 810, XP002944464, ISSN: 0002-9297 *

Also Published As

Publication number Publication date
WO2002035442A2 (en) 2002-05-02
EP1350212A2 (en) 2003-10-08

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