Supplementary Figure 2: Principal component analysis (PCA) of the Russian GWAS samples | Nature Genetics

Supplementary Figure 2: Principal component analysis (PCA) of the Russian GWAS samples

From: Susceptibility to tuberculosis is associated with variants in the ASAP1 gene encoding a regulator of dendritic cell migration

Supplementary Figure 2

(a) First and second principal components. Russian samples are plotted with ten HapMap3 populations (ASW – African ancestry in Southwest USA; CEU – Utah residents of European ancestry; CHB – Han Chinese in Beijing, China; CHD – Chinese in Metropolitan Denver, Colorado; JPT – Japanese in Tokyo, Japan; GIH – Gujarati Indians in Houston, Texas; LWK – Luhya in Webuye, Kenya; MKK – Maasai in Kinyawa, Kenya; TSI – Tuscans in Italy; YRI – Yoruba in Ibadan, Nigeria).

(b) All GWAS samples plotted on the first two principal components colored by the city of sample origin.

(c) Russian TB cases and controls projected onto the first two principal components using SNP weights precomputed from European samples in the 1000 Genomes Phase III project (CEU — Utah residents with Northern and Western European ancestry; IBS — Iberian populations in Spain; FIN — Finnish in Finland; GBR — British in England and Scotland; and TSI — Toscani in Italy) using SNPweights (Chen, C.Y. et al. Improved ancestry inference using weights from external reference panels. Bioinformatics 29, 1399-1406 (2013)).

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