HapMap tagSNP transferability in multiple populations: general guidelines - PubMed (original) (raw)

HapMap tagSNP transferability in multiple populations: general guidelines

Jinchuan Xing et al. Genomics. 2008 Jul.

Abstract

Linkage disequilibrium (LD) has received much attention recently because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian sample and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r(2) >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations.

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Figures

Figure 1

Figure 1. Populations examined

Number of individuals in each population sample is given in parentheses.

Figure 2

Figure 2. Correlations of allele frequencies (A) and LD measures (_r_2) for all SNP pairs (B) between HapMap populations and corresponding continental groups

Spearman’s correlations (rho) are shown.

Figure 3

Figure 3. Correlation of allele frequency between HapMap populations and A) Indians; B) Mbuti Pygmies

Spearman’s correlations (rho) are shown.

Figure 4

Figure 4. Correlation of pairwise LD (_r_2) between HapMap populations and A) Indians; B) Mbuti Pygmies

Spearman’s correlations (rho) are shown.

Figure 5

Figure 5. HapMap tagSNP transferability and tagging efficiency

(A) HapMap tagSNP transferability in three continental groups (AFR, EAS and EUR) and two populations (IND and PYG) are shown. The average transferability among all 14 regions are shown as bars, and the transferability for each individual region are shown as black dots. For example, the first blue bar in the “AFR” section indicates that tagSNPs selected from the HapMap CEU population captured ~60% of the SNPs with _r_2 >= 0.8 in our Africans, on average. (B) HapMap tagSNP tagging efficiency. The average tagging efficiency across all 14 regions are shown as bars, and the tagging efficiencies for each region are shown as black dots. For example, the last brown bar in the “PYG” section indicates that on average every HapMap YRI tagSNPs captured 1.21 SNPs in our African Pygmy samples.

Figure 6

Figure 6

A flow chart for tagSNP selection using HapMap populations.

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