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

Laura M. Huckins* (Corresponding Author), Vesna Boraska, Christopher S. Franklin, James A.B. Floyd, Lorraine Southam, GCAN, WTCCC3, Patrick F. Sullivan, Cynthia M. Bulik, David A. Collier, Chris Tyler-Smith, Eleftheria Zeggini, Ioanna Tachmazidou

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1190-1200
Number of pages11
JournalEuropean Journal of Human Genetics
Issue number10
Publication statusPublished - 11 Oct 2014

Bibliographical note

Funding Information:
LMH, VB, CSF, JABF, LS, CTS, IT and EZ were supported by the Wellcome Trust (098051). LMH is also supported by the MRC (MR/J500355/1), VB is also supported by Unity Through Knowledge Fund CONNECTIVITY PROGRAM (‘Gaining Experience’ Grant 2A), The National Foundation for Science, Higher Education and Technological Development of the Republic of Croatia (BRAIN GAIN-Postdoc fellowship) and CMB is supported by the Foundation of Hope.

Publisher Copyright:
© 2014 Macmillan Publishers Limited All rights reserved.


  • AIMs
  • population stratification
  • principal component analysis


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