A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors

MacLeod, I. M., Meuwissen, T. H. E., Hayes, B. J. and Goddard, M. E. (2009) A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors. Genetics Research, 91 6: 413-426. doi:10.1017/S0016672309990358


Author MacLeod, I. M.
Meuwissen, T. H. E.
Hayes, B. J.
Goddard, M. E.
Title A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors
Journal name Genetics Research   Check publisher's open access policy
ISSN 0016-6723
Publication date 2009-12
Sub-type Article (original research)
DOI 10.1017/S0016672309990358
Open Access Status Not yet assessed
Volume 91
Issue 6
Start page 413
End page 426
Total pages 14
Place of publication Cambridge, United Kingdom
Publisher Cambridge University Press
Language eng
Formatted abstract
The patterns of linkage disequilibrium (LD) between dense polymorphic markers are shaped by the ancestral population history. It is therefore possible to use multilocus predictors of LD to infer past population history and to infer sharing of identical alleles in quantitative trait locus (QTL) studies. We develop a multilocus predictor of LD for pairs of haplotypes, which we term haplotype homozygosity (HHn): the probability that any two haplotypes share a given number of n adjacent identical markers or runs of homozygosity. Our method, based on simplified coalescence theory, accounts for recombination and mutation. We compare our HHn predictions, with HHn in simulated populations and with two published predictors of HHn. Our method performs consistently better across a range of population parameters, including populations with a severe bottleneck followed by expansion, compared to two published methods. We demonstrate that we can predict the pattern of HHn observed in dense single nucleotide polymorphisms (SNPs) genotyped in a cattle population, given appropriate historical changes in population size. Our method is practical for use with very large numbers of individuals and dense genome wide polymorphic DNA data. It has potential applications in inferring ancestral population history and QTL mapping studies.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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