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Using ancestry-informative markers to identify fine structure across 15 populations of European origin.

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Huckins, Laura M 
Boraska, Vesna 
Franklin, Christopher S 
Floyd, James AB 
Southam, Lorraine 


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.



Anorexia Nervosa, Gene Frequency, Genetic Markers, Genetics, Population, Genome-Wide Association Study, Genotyping Techniques, Humans, Oligonucleotide Array Sequence Analysis, Phylogeography, Polymorphism, Single Nucleotide, Principal Component Analysis, Reproducibility of Results, Sample Size, White People

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Eur J Hum Genet

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Springer Science and Business Media LLC
British Heart Foundation (None)