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HapMap phase 3 data available for browsing

By dgmacarthur on September 19, 2008.

i-bafc1078cd52232da434a3620640cd2d-hapmap3.jpg

This will probably only be of interest to population genetics afficianados, but I just noticed that the HapMap project has made its phase 3 data available through its browser (the data were previously available for download, but are much more accessible - especially to non-bioinformaticians - through the browser interface).

The HapMap project is a massive international collaboration collecting information on common sites of genetic variation (called single nucleotide polymorphisms, or SNPs) in anonymised individuals from a variety of human populations. Phase 3 has data on about 1.5 million genetic markers for 1,115 individuals from 11 populations. That's substantially fewer markers than in earlier phases of the HapMap project, but on a hugely expanded set of samples (the original HapMap data-set contained information on just 270 individuals from 4 populations). Of particular interest are three additional populations with African ancestry (Luhya and Maasai from Kenya, and African-Americans collected in southwest USA), given the exceptionally high level of genetic diversity in African groups relative to other human populations.

This is still very much a rough draft of the catalogue of human genetic diversity, sampling just a tiny fraction of our species' populations and being restricted only to common genetic variants. Extending the catalogue to include rare variants will require whole-genome sequencing of much larger samples - work that is currently being kick-started by the ambitious 1000 Genomes Project.

The breakdown of the analysed samples in the phase 3 HapMap data-set is below the fold...

Number CodePopulation
71ASWAfrican ancestry in Southwest USA
162CEUUtah residents with European ancestry
82CHBHan Chinese in Beijing, China
70CHDChinese in Metropolitan Denver, Colorado
83GIHGujarati Indians in Houston, Texas
82JPTJapanese in Tokyo, Japan
83LWKLuhya in Webuye, Kenya
71MEXMexican ancestry in Los Angeles, California
171MKKMaasai in Kinyawa, Kenya
77TSIToscani in Italia
163YRIYoruba in Ibadan, Nigeria
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big genetics

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