Whole genome identity-by-descent determination

Sabaa, Hadi, Cai, Zhipeng, Wang, Yining, Goebel, Randy, Moore, Stephen and Lin, Guohui (2013) Whole genome identity-by-descent determination. Journal of Bioinformatics and Computational Biology, 11 2: . doi:10.1142/S0219720013500029

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Author Sabaa, Hadi
Cai, Zhipeng
Wang, Yining
Goebel, Randy
Moore, Stephen
Lin, Guohui
Title Whole genome identity-by-descent determination
Journal name Journal of Bioinformatics and Computational Biology   Check publisher's open access policy
ISSN 0219-7200
Publication date 2013-01-01
Year available 2013
Sub-type Article (original research)
DOI 10.1142/S0219720013500029
Open Access Status Not yet assessed
Volume 11
Issue 2
Total pages 19
Place of publication London, United Kingdom
Publisher Imperial College Press
Language eng
Subject 1303 Specialist Studies in Education
1312 Molecular Biology
1706 Computer Science Applications
Abstract High-throughput single nucleotide polymorphism genotyping assays conveniently produce genotype data for genome-wide genetic linkage and association studies. For pedigree datasets, the unphased genotype data is used to infer the haplotypes for individuals, according to Mendelian inheritance rules. Linkage studies can then locate putative chromosomal regions based on the haplotype allele sharing among the pedigree members and their disease status. Most existing haplotyping programs require rather strict pedigree structures and return a single inferred solution for downstream analysis. In this research, we relax the pedigree structure to contain ungenotyped founders and present a cubic time whole genome haplotyping algorithm to minimize the number of zero-recombination haplotype blocks. With or without explicitly enumerating all the haplotyping solutions, the algorithm determines all distinct haplotype allele identity-by-descent (IBD) sharings among the pedigree members, in linear time in the total number of haplotyping solutions. Our algorithm is implemented as a computer program iBDD. Extensive simulation experiments using 2 sets of 16 pedigree structures from previous studies showed that, in general, there are trillions of haplotyping solutions, but only up to a few thousand distinct haplotype allele IBD sharings. iBDD is able to return all these sharings for downstream genome-wide linkage and association studies.
Keyword Haplotype allele sharing
Identical by descent
Linkage analysis
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2014 Collection
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Citation counts: TR Web of Science Citation Count  Cited 4 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 7 times in Scopus Article | Citations
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Created: Thu, 28 Nov 2013, 22:44:32 EST by System User on behalf of Qld Alliance for Agriculture and Food Innovation