AI Article Synopsis
- The Wellcome Trust Case Control Consortium 3 conducted a genome-wide association scan for anorexia nervosa using 2,907 cases from 15 European populations and the Illumina 670K chip.
- The study compared different methods to identify population stratification, suggesting that using all SNPs with a minor allele frequency (MAF) greater than 1% could be more effective than the usual threshold of 5%.
- Principal component analysis revealed significant genetic variation across the populations, helping to identify hidden stratification and offering insights for better designing and interpreting association studies in international research efforts.
Article Abstract
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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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169539 | PMC |
| http://dx.doi.org/10.1038/ejhg.2014.1 | DOI Listing |
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