Recent studies by our group and others have led to the identification of SNP subsets that can provide European substructure information [6,7]; this is consistent with previous work suggesting distinct clines of genetic variation within Europe [15–20]. These European substructure ancestry informative markers (ESAIMs) may be particularly important in large replication studies in which independent sets of case and control genotypes are necessary to confirm and further define associations without the benefit of genome-wide SNP typing. Previous studies have been limited to initial SNP genotyping sets of less than 10,000 SNPs [6,7]. The current study uses 300K to 500K genome-wide SNP data to enhance the ability to define elements of European substructure that were not evident or poorly defined using smaller sets of SNPs.
