One individual and 20,847 SNVs were removed due to low genotype call rates (individuals or SNVs with call rates < 95%), and 190,855 monomorphic SNVs were excluded. Following tests for deviations from Hardy-Weinberg equilibrium, 1,028 SNVs with a p-value less than 1e-07 were removed. All duplicate markers, mitochondrial markers and markers on sex chromosomes were excluded (n = 13,005 SNVs). Cross-referencing allele frequencies with the European sample for the 1,000 Genomes Project (The 1000 Genomes Project Consortium, 2012) resulted in the exclusion of 381 SNVs, whose allele frequencies differed more than 0.20 from this reference panel. Following the completion of standard quality control procedures, 497 individuals and 393,812 SNVs remained in the dataset. In order to capture non-typed genetic variation, genotype pre-phasing was conducted using the SHAPEIT2 program, followed by genome-wide imputation using the 1000 Genomes Project reference haplotype panels with IMPUTE2 (Howie et al., 2009). The latter programs do not allow for the inclusion of indels, and therefore all simple and complex indels (n = 8,751) were excluded prior to genotype pre-phasing and imputation. Finally, ancestry estimations were calculated
