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WO2002064617A3 - Method and system for haplotype reconstruction - Google Patents

Method and system for haplotype reconstruction Download PDF

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Publication number
WO2002064617A3
WO2002064617A3 PCT/US2002/003486 US0203486W WO02064617A3 WO 2002064617 A3 WO2002064617 A3 WO 2002064617A3 US 0203486 W US0203486 W US 0203486W WO 02064617 A3 WO02064617 A3 WO 02064617A3
Authority
WO
WIPO (PCT)
Prior art keywords
information
haplotype
conditional distribution
genotype
derived
Prior art date
Application number
PCT/US2002/003486
Other languages
French (fr)
Other versions
WO2002064617A2 (en
Inventor
Matthew Stephens
Peter James Donnelly
Nicholas James Smith
Original Assignee
Isis Innovation
Matthew Stephens
Peter James Donnelly
Nicholas James Smith
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 Isis Innovation, Matthew Stephens, Peter James Donnelly, Nicholas James Smith filed Critical Isis Innovation
Priority to AU2002243860A priority Critical patent/AU2002243860A1/en
Publication of WO2002064617A2 publication Critical patent/WO2002064617A2/en
Publication of WO2002064617A3 publication Critical patent/WO2002064617A3/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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

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

Abstract

A method for determining haplotype information from genotype information on individuals in a sample, comprises the steps of: executing a Markov chain Monte Carlo algorithm to derive information on the conditional distribution of haplotypes, based on the genotype information; and estimating haplotype information using the derived information on the conditional distribution. The method can also be used to quantify the uncertainty associated with the estimated haplotype information, using the derived information on the conditional distribution.
PCT/US2002/003486 2001-02-09 2002-02-08 Method and system for haplotype reconstruction WO2002064617A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002243860A AU2002243860A1 (en) 2001-02-09 2002-02-08 Method and system for haplotype reconstruction

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GB0103295.2 2001-02-09
GBGB0103295.2A GB0103295D0 (en) 2001-02-09 2001-02-09 Method and system for haplotype reconstruction

Publications (2)

Publication Number Publication Date
WO2002064617A2 WO2002064617A2 (en) 2002-08-22
WO2002064617A3 true WO2002064617A3 (en) 2003-02-27

Family

ID=9908468

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/003486 WO2002064617A2 (en) 2001-02-09 2002-02-08 Method and system for haplotype reconstruction

Country Status (3)

Country Link
AU (1) AU2002243860A1 (en)
GB (1) GB0103295D0 (en)
WO (1) WO2002064617A2 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7058517B1 (en) 1999-06-25 2006-06-06 Genaissance Pharmaceuticals, Inc. Methods for obtaining and using haplotype data
US6931326B1 (en) 2000-06-26 2005-08-16 Genaissance Pharmaceuticals, Inc. Methods for obtaining and using haplotype data
FR2939929A1 (en) 2008-12-11 2010-06-18 Conservatoire Nat Arts METHOD FOR COMPUTER-BASED CALCULATION OF THE PROBABILITY OF OBSERVING DIFFERENT SEQUENCES OF ARRANGEMENTS OF STATES OBSERVED WITH A VARIABLE MODELIZED BY A MARKOV CACHE MODEL

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6291182B1 (en) * 1998-11-10 2001-09-18 Genset Methods, software and apparati for identifying genomic regions harboring a gene associated with a detectable trait
US20020077775A1 (en) * 2000-05-25 2002-06-20 Schork Nicholas J. Methods of DNA marker-based genetic analysis using estimated haplotype frequencies and uses thereof

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6291182B1 (en) * 1998-11-10 2001-09-18 Genset Methods, software and apparati for identifying genomic regions harboring a gene associated with a detectable trait
US20020077775A1 (en) * 2000-05-25 2002-06-20 Schork Nicholas J. Methods of DNA marker-based genetic analysis using estimated haplotype frequencies and uses thereof

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
SILLANPAA ET AL.: "Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data", GENETICS, vol. 151, April 1999 (1999-04-01), pages 1605 - 1619, XP002951282 *
THOMAS ET AL.: "A bayesian approach to multipoint mapping in nuclear families", GENETIC EPIDEMIOLOGY, vol. 14, no. 6, 1997, pages 903 - 908, XP002951283 *

Also Published As

Publication number Publication date
GB0103295D0 (en) 2001-03-28
WO2002064617A2 (en) 2002-08-22
AU2002243860A1 (en) 2002-08-28

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