HGDP iHS Track Settings
 
Human Genome Diversity Project Integrated Haplotype Score on 7 Continents   (All Variation and Repeats tracks)

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

Description

This track shows per-continent integrated haplotype score (iHS, Voight et al.), a measure of very recent positive selection. 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. iHS was then calculated for each population group using the program ihs (source code available) and then normalizing the resulting unstandardized iHS scores in derived allele frequency bins as described in (Voight et al.). Per-SNP iHS scores were smoothed in windows of 31 SNPs, centered on each SNP. The final score is -log10 of the proportion of smoothed scores higher than each SNP's smoothed score.

Credits

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

References

Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol. 2006 Mar;4(3):e72.

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.