Abstract
Several studies of haplotype structures in the human genome in various populations have found that the human chromosomes are structured such that each chromosome can be divided into many blocks, within which there is limited haplotype diversity. In addition, only a few genetic markers in a putative block are needed to capture most of the diversity within a block. There has been no systematic empirical study of the effects of sample size and marker set on the identified block structures and representative marker sets, however. The purpose of this study was to conduct a detailed empirical study to examine such impacts. Towards this goal, we have analysed three representative autosomal regions from a large genome-wide study of haplotypes with samples consisting of African-Americans and samples consisting of Japanese and Chinese individuals. For both populations, we have found that the sample size and marker set have significant impact on the number of blocks and the total number of representative markers identified. The marker set in particular has very strong impacts, and our results indicate that the marker density in the original datasets may not be adequate to allow a meaningful characterisation of haplotype structures. In general, we conclude that we need a relatively large sample size and a very dense marker panel in the study of haplotype structures in human populations.
Highlights
Human DNA sequence variation accounts for a large fraction of the observed phenotypic differences between individuals, including susceptibility to disease
We focused on the impact of sample size and single nucleotide polymorphisms (SNPs) marker selection on the haplotype block partitioning and Tag SNP selections in a sample consisting of African-Americans and a sample consisting of Japanese and Chinese people
In order to examine the impact of sample size and marker selection on haplotype block boundaries and Tag SNPs, three regions from the above database were chosen in our study
Summary
Human DNA sequence variation accounts for a large fraction of the observed phenotypic differences between individuals, including susceptibility to disease. Sites in the DNA sequence where individuals differ at a single DNA base are called single nucleotide polymorphisms (SNPs). Linked SNPs are not independent on a given chromosome, but tend to be associated with each other across small regions. Empirical data suggest that relatively few of the theoretically possible haplotypes are observed at significant frequencies for a set of SNPs within a very short physical distance.[4]
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