HGDP XP-EHH Track Settings
 
Human Genome Diversity Proj Cross-Pop Ext Haplo Homzgty (XP-EHH) on 7 Continents   (All Variation and Repeats tracks)

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 XP-EHH Bantu  Human Genome Diversity Project XP-EHH (Bantu populations in Africa)   Schema 
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 XP-EHH Mideast  Human Genome Diversity Project XP-EHH (Mideast)   Schema 
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 XP-EHH Europe  Human Genome Diversity Project XP-EHH (Europe)   Schema 
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 XP-EHH S. Asia  Human Genome Diversity Project XP-EHH (South Asia)   Schema 
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 XP-EHH E. Asia  Human Genome Diversity Project XP-EHH (East Asia)   Schema 
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 XP-EHH Oceania  Human Genome Diversity Project XP-EHH (Oceania)   Schema 
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 XP-EHH Americas  Human Genome Diversity Project XP-EHH (Americas)   Schema 
    

Description

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 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. 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 xpehh (source code available) as described in Sabeti et al.

Credits

Thanks to the HGDP-CEPH and Joe Pickrell in the Pritchard lab at the University of Chicago for providing these data.

References

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.