In order to investigate in detail the genetic structure of the Baltic countries and neighbouring North-Eastern Europe, whole genome genotyping was undertaken for over 1,000 Estonians and additional individuals from Bulgaria, the Czech Republic, Hungary, Latvia, Lithuania, Poland and Russia, using the Illumina Human370CNV chip. In addition, raw genotyping data were obtained from Scandinavia and other Western and Northern European countries (Table 1). From samples with >100 individuals available (Table 1), a sub-set of 100 individuals was chosen at random for subsequent analyses in order to minimize sample size effects. In all instances, the inflation factor λ as computed for the complete data set versus the random sub-set was close to unity, indicating that the latter sets were representative of the entire samples. In total, genotypes of 273,464 SNPs from 1,564 individuals were included in the statistical analyses.
