Abstract
The definition of European population genetic substructure and its application to
understanding complex phenotypes is becoming increasingly important. In the current study
using over 4000 subjects genotyped for 300 thousand SNPs we provide further insight into
relationships among European population groups and identify sets of SNP ancestry
informative markers (AIMs) for application in genetic studies. In general, the graphical
description of these principal components analyses (PCA) of diverse European subjects
showed a strong correspondence to the geographical relationships of specific countries or
regions of origin. Clearer separation of different ethnic and regional populations was
observed when northern and southern European groups were considered separately and the PCA
results were influenced by the inclusion or exclusion of different self-identified
population groups including Ashkenazi Jewish, Sardinian and Orcadian ethnic groups. SNP
AIM sets were identified that could distinguish the regional and ethnic population groups.
Moreover, the studies demonstrated that most allele frequency differences between
different European groups could be effectively controlled in analyses using these AIM
sets. The European substructure AIMs should be widely applicable to ongoing studies to
confirm and delineate specific disease susceptibility candidate regions without the
necessity to perform additional genome-wide SNP studies in additional subject sets.