Tuesday, October 31, 2006

HapMap of three population groups not too shabby

A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

Donald F Conrad, Mattias Jakobsson, Graham Coop, Xiaoquan Wen, Jeffrey D Wall, Noah A Rosenberg & Jonathan K Pritchard

Nature Genetics 38, 1251 - 1260 (2006)

Abstract: Recent genomic surveys have produced high-resolution haplotype information, but only in a small number of human populations. We report haplotype structure across 12 Mb of DNA sequence in 927 individuals representing 52 populations. The geographic distribution of haplotypes reflects human history, with a loss of haplotype diversity as distance increases from Africa. Although the extent of linkage disequilibrium (LD) varies markedly across populations, considerable sharing of haplotype structure exists, and inferred recombination hotspot locations generally match across groups. The four samples in the International HapMap Project contain the majority of common haplotypes found in most populations: averaging across populations, 83% of common 20-kb haplotypes in a population are also common in the most similar HapMap sample. Consequently, although the portability of tag SNPs based on the HapMap is reduced in low-LD Africans, the HapMap will be helpful for the design of genome-wide association mapping studies in nearly all human populations.

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