Journal
EUROPEAN JOURNAL OF HUMAN GENETICS
Volume 22, Issue 10, Pages 1190-1200Publisher
SPRINGERNATURE
DOI: 10.1038/ejhg.2014.1
Keywords
population stratification; AIMs; principal component analysis
Funding
- Wellcome Trust [098051]
- MRC [MR/J500355/1]
- Unity Through Knowledge Fund CONNECTIVITY PROGRAM ('Gaining Experience' ) [2A]
- National Foundation for Science, Higher Education and Technological Development of the Republic of Croatia (BRAIN GAIN- Postdoc fellowship)
- Foundation of Hope
- British Heart Foundation [RG/09/012/28096] Funding Source: researchfish
- Medical Research Council [MR/K500999/1, MR/J006742/1] Funding Source: researchfish
- National Institute for Health Research [NF-SI-0510-10214, RP-PG-0310-1002, NF-SI-0513-10151] Funding Source: researchfish
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The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia.
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