The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection

Ding, Keyue and Zhou, Kaixin and Zhang, Jing and Knight, Joanne and Zhang, Xuegong and Shen, Yan (2005) The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection. Molecular Biology and Evolution, 22 (1). pp. 148-159. ISSN 0737-4038

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Abstract

It has been recently suggested that the human genome is organized as a series of haplotype blocks, and efforts to create a genome-wide haplotype map are already underway. Several computational algorithms have been proposed to partition the genome. However, little is known about their behaviors in relation to the haplotype-block partitioning and haplotype-tagging SNPs selection. Here, we present a systematic comparison of three classes of haplotype-block partition definitions, a diversity-based method, a linkage-disequilibrium (LD)-based method, and a recombination-based method. The data used were derived from a coalescent simulation under both a uniform recombination model and one that assumes recombination hotspots. There were considerable differences in haplotype information loss in the measure of entropy when the partition methods were compared under different population-genetics scenarios. Under both recombination models, the results from the LD-based definition and the recombination-based definition were more similar to each other than were the results from the diversity-based definition. This work demonstrates that when undertaking haplotype-based association mapping, the choice of haplotype-block definition and SNP selection requires careful consideration.

Item Type: Journal Article
Journal or Publication Title: Molecular Biology and Evolution
Uncontrolled Keywords: /dk/atira/pure/subjectarea/asjc/1300/1312
Subjects:
ID Code: 79934
Deposited By: ep_importer_pure
Deposited On: 07 Jun 2016 12:54
Refereed?: Yes
Published?: Published
Last Modified: 01 Jan 2020 09:47
URI: https://eprints.lancs.ac.uk/id/eprint/79934

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