WO2004031912A3 - Methods for estimating haplotype frequencies and disease associations with haplotypes and environmental variables - Google Patents

Methods for estimating haplotype frequencies and disease associations with haplotypes and environmental variables Download PDF

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Publication number
WO2004031912A3
WO2004031912A3 PCT/US2003/031186 US0331186W WO2004031912A3 WO 2004031912 A3 WO2004031912 A3 WO 2004031912A3 US 0331186 W US0331186 W US 0331186W WO 2004031912 A3 WO2004031912 A3 WO 2004031912A3
Authority
WO
WIPO (PCT)
Prior art keywords
methods
haplotypes
estimating
haplotype frequencies
environmental variables
Prior art date
Application number
PCT/US2003/031186
Other languages
French (fr)
Other versions
WO2004031912A2 (en
Inventor
Lue Ping Zhao
Original Assignee
Hutchinson Fred Cancer Res
Lue Ping Zhao
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 Hutchinson Fred Cancer Res, Lue Ping Zhao filed Critical Hutchinson Fred Cancer Res
Priority to AU2003282907A priority Critical patent/AU2003282907A1/en
Publication of WO2004031912A2 publication Critical patent/WO2004031912A2/en
Publication of WO2004031912A3 publication Critical patent/WO2004031912A3/en

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Classifications

    • 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
    • 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
    • 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

Abstract

The invention provides methods for estimating haplotype frequencies using an estimating equation method and a forward-block algorithm that provides a standard error measurement for each estimated haplotype frequency. The methods may be used, for example, for estimating a set of haplotype frequencies in a population, for assessing the association of a haplotype with a trait, and for assessing the association of haplotypes for one or more set of markers and one or more environmental factors with a trait. The invention also provides a computer-readable medium having computer-readable instructions for performing the methods of the invention, and a computer-system for performing the methods of the invention.
PCT/US2003/031186 2002-10-01 2003-10-01 Methods for estimating haplotype frequencies and disease associations with haplotypes and environmental variables WO2004031912A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2003282907A AU2003282907A1 (en) 2002-10-01 2003-10-01 Methods for estimating haplotype frequencies and disease associations with haplotypes and environmental variables

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US41502802P 2002-10-01 2002-10-01
US60/415,028 2002-10-01

Publications (2)

Publication Number Publication Date
WO2004031912A2 WO2004031912A2 (en) 2004-04-15
WO2004031912A3 true WO2004031912A3 (en) 2004-08-05

Family

ID=32069800

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2003/031186 WO2004031912A2 (en) 2002-10-01 2003-10-01 Methods for estimating haplotype frequencies and disease associations with haplotypes and environmental variables

Country Status (2)

Country Link
AU (1) AU2003282907A1 (en)
WO (1) WO2004031912A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9170992B2 (en) 2007-03-16 2015-10-27 Expanse Bioinformatics, Inc. Treatment determination and impact analysis

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090043752A1 (en) 2007-08-08 2009-02-12 Expanse Networks, Inc. Predicting Side Effect Attributes
US8200509B2 (en) 2008-09-10 2012-06-12 Expanse Networks, Inc. Masked data record access
US7917438B2 (en) 2008-09-10 2011-03-29 Expanse Networks, Inc. System for secure mobile healthcare selection
US8108406B2 (en) 2008-12-30 2012-01-31 Expanse Networks, Inc. Pangenetic web user behavior prediction system
EP3276526A1 (en) 2008-12-31 2018-01-31 23Andme, Inc. Finding relatives in a database
WO2012034030A1 (en) * 2010-09-09 2012-03-15 Omicia, Inc. Variant annotation, analysis and selection tool
EP2929070A4 (en) * 2012-12-05 2016-06-01 Genepeeks Inc System and method for the computational prediction of expression of single-gene phenotypes
WO2014144032A2 (en) * 2013-03-15 2014-09-18 The Broad Institute, Inc. Systems and methods for identifying significantly mutated genes

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
DRYSDALE C.M. ET AL: "Complex promoter and coding region beta2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness", PNAS, vol. 97, no. 19, 12 September 2000 (2000-09-12), pages 10483 - 10488, XP002940094 *
EXCOFFIER L. ET AL: "Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population", MOLECULAR BIOLOGY AND EVOLUTION, vol. 12, no. 5, 1995, pages 921 - 927, XP002953528 *
FALLIN D. ET AL: "Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data", J. OF HUMAN GENETICS, vol. 67, October 2000 (2000-10-01), pages 947 - 959, XP002951850 *
NIU T. ET AL: "Bayesian haplotype inference for multiple linked single-nucleotide polymophisms", AM.J. OF HUMAN GENETICS, vol. 70, January 2002 (2002-01-01), pages 157 - 169, XP002978163 *
PATIL N. ET AL: "Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21", SCIENCE, vol. 294, 23 November 2001 (2001-11-23), pages 1719 - 1723, XP002965310 *
STEPHENS M. ET AL: "A new statistical method for haplotype reconstruction from population data", AM. J. OF HUMAN GENETICS, vol. 68, April 2001 (2001-04-01), pages 978 - 989, XP002955780 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9170992B2 (en) 2007-03-16 2015-10-27 Expanse Bioinformatics, Inc. Treatment determination and impact analysis
US9582647B2 (en) 2007-03-16 2017-02-28 Expanse Bioinformatics, Inc. Attribute combination discovery for predisposition determination

Also Published As

Publication number Publication date
AU2003282907A8 (en) 2004-04-23
AU2003282907A1 (en) 2004-04-23
WO2004031912A2 (en) 2004-04-15

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