This track shows per-continent Cross Population Extended Haplotype
Homozygosity (XP-EHH) score (Sabeti et al.), an estimate of
positive selection that highlights SNPs that have approached or
achieved fixation in a population but remain polymorphic in the human
population as a whole.
Scores were calculated using SNPs genotyped in 53 populations worldwide by the
Genome Diversity Project in collaboration with the
du Polymorphisme Humain (HGDP-CEPH).
This track and several others are available from the
HGDP Selection Browser.
Samples collected by the HGDP-CEPH from 1,043 individuals from around the
world were genotyped for 657,000 SNPs at
The 53 populations were divided into seven continental groups: Africa
(Bantu populations only),
Middle East, Europe, South Asia, East Asia, Oceania and the Americas.
Bantu populations in Africa were chosen instead of all African populations
because a more closely related group was desired for comparison with
other continental groups.
XP-EHH was then calculated for each population group using the program
(source code available)
as described in Sabeti et al.
Thanks to the HGDP-CEPH and Joe Pickrell in the
lab at the University of Chicago for providing these data.
Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C,
Xie X, Byrne EH, McCarroll SA, Gaudet R et al.
Genome-wide detection and characterization of positive
selection in human populations.
Nature. 2007 Oct 18;449(7164):913-8.
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.
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.
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.