## Description

This track shows the 657,000 SNPs genotyped in 53 populations worldwide by the Human Genome Diversity Project in collaboration with the Centre d'Etude du Polymorphisme Humain (HGDP-CEPH). This track and several others are available from the HGDP Selection Browser.

## Methods

Samples collected by the HGDP-CEPH from 1,043 individuals from around the world were genotyped for 657,000 SNPs at Stanford. Ancestral states for all SNPs were estimated using whole genome human-chimpanzee alignments from the UCSC database. For each SNP in the human genome (NCBI Build 35, UCSC database hg17), the allele at the corresponding position in the chimp genome (Build 2 version 1, UCSC database pantro2) was used as ancestral.

Allele frequencies were plotted on a world map using programs included in the Generic Mapping Tools.

## Credits

Thanks to the HGDP-CEPH, the Pritchard lab at the University of Chicago, Joe Pickrell and John Novembre for sharing the data and plotting scripts for this track.

## References

Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A et al. A human genome diversity cell line panel. Science. 2002 Apr 12;296(5566):261-2.

Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM. Worldwide human relationships inferred from genome-wide patterns of variation. Science. 2008 Feb 22;319(5866):1100-4.

Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li J, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 2009 May;19(5):826-37.

Wessel P, Smith WHF. New, improved version of Generic Mapping Tools released. EOS, Trans. Amer. Geophys. U. 1998;79(47):579.