Open Access Highly Accessed Research article

Worldwide population differentiation at disease-associated SNPs

Sean Myles15*, Dan Davison2, Jeffrey Barrett3, Mark Stoneking1 and Nic Timpson34

Author Affiliations

1 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany

2 Department of Statistics, Oxford University, 1 South Parks Road, Oxford, OX1 3TG, UK

3 Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK

4 MRC CAiTE Centre, Department of Social Medicine, University of Bristol, Canynge Hall, Whiteladies Road, Bristol, BS8 2PR, UK

5 Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY 14853-2703, USA

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BMC Medical Genomics 2008, 1:22  doi:10.1186/1755-8794-1-22

Published: 4 June 2008

Additional files

Additional file 1:

Correlation between minor allele frequency and global Fst for 2750 markers typed in 927 individuals from the CEPH-HGDP panel.

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Additional file 2:

Global Fst density distributions for 2750 markers typed in the 927 individuals from the CEPH-HGDP panel divided into 5 bins according to minor allele frequency.

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Additional file 3:

Worldwide risk allele frequencies and population differentiation for 25 disease-associated SNPs. The dbSNP ID and disease for each SNP is found at the top of each figure. Risk allele frequencies were calculated using data from 952 individuals from the CEPH-HGDP panel and are displayed in the vertical bar chart with sample size in number of individuals to the left. Pairwise Fst values for the 53 × 53 population matrix and the 7 × 7 geographical region matrix were calculated using data from the same 927 individuals who were used to generate the empirical distribution. Each square in the 53 × 53 and 7 × 7 matrices represents a pairwise Fst comparison between populations and geographic regions, respectively. The shaded boxes in the matrices indicate which pairwise Fst values are significant compared to the empirical distribution at three P value thresholds (see the boxed-in P value legend of Figure 2).

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