HGDP Smoothd FST Track Settings
 
Human Genome Diversity Project Smoothed Relative FST (Fixation Index)   (All Variation and Repeats tracks)

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Data last updated at UCSC: 2009-02-12

Description

In this track, the value shown for each SNP is -log10 of the fraction of SNPs with a more extreme FST value than that SNP. Relative FST (also known as the Fixation index) values were calculated from 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.

From Wikipedia:

Fixation index (FST) is a measure of population differentiation based on genetic polymorphism data, such as Single nucleotide polymorphisms (SNPs) or microsatellites. It is a special case of F-statistics, the concept developed in the 1920s by Sewall Wright. This statistic compares the genetic variability within and between populations and is frequently used in the field of population genetics.
From http://www.uwyo.edu/dbmcd/popecol/Maylects/PopGenGloss.html:
FST is the proportion of the total genetic variance contained in a subpopulation (the S subscript) relative to the total genetic variance (the T subscript). Values can range from 0 to 1. High FST implies a considerable degree of differentiation among populations.

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, Middle East, Europe, South Asia, East Asia, Oceania and the Americas. FST was computed for all SNPs, and then each SNP's place in the empirical FST distribution was used to derive the scores shown in this track, -log10 of the fraction of SNPs with a more extreme FST value than that SNP.

Credits

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

References

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.