Phase III of the human HapMap released

8 September 2010

The third instalment of the human HapMap, a catalogue of common human genetic variation, has been published in Nature  [The International HapMap Consortium (2010), Nature 467: 52-58]. 

The International HapMap consortium was launched in 2002, with the goal of “compare[ing] the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared”. The first phase was published in 2005 (see previous news), with around a million single nucleotide polymorphisms (SNPs) from 269 individuals from Africa, China, Japan and Western Europe, to which a further 2 million SNPs were added two years later (see previous news). HapMap3 casts the net even wider and includes 1.6 million SNPs from 1,184 individuals from 11 global populations. In addition, ten 100-kilobase ENCODE regions were fully sequenced in 692 of these individuals, allowing integration of both common and rare alleles, including both SNPs and copy number polymorphisms (CNPs).

Although common variants (present in >5% of the population) are shared across global populations and can be well assayed using standard genotyping chips, rarer variants are generally population specific and are currently inadequately sampled as they require deep sequencing. The authors state that this finding highlights “the importance of sampling widely to achieve a comprehensive understanding of human variation.” Providing a higher resolution catalogue with broader population coverage will no doubt improve the interpretation of genome-wide association studies, and inform the design of full sequencing projects such as the 1000 Genomes Project.


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