File:PCA results highlighting differences in genetic make-up across the Netherlands.jpg

English: Genomic structure of the Netherlands. PCA results highlighting differences in genetic make-up across the Netherlands: the plots give PC1 versus PC2, and PC1 versus PC3.

To describe the regional genomic differences in the genetic make-up across the Netherlands, principal component analysis (PCA) was run using the EIGENSOFT package. The PCA was first run on 4441 unrelated Dutch individuals typed on the Affymetrix Human Genome-Wide SNP 6.0 Array (Affymetrix Inc., Santa Clara, CA, USA), with a SNP set excluding 24 long-range LD regions and LD-based SNP pruning (based on a variance inflation factor of 2), resulting in a set of 130 248 SNPs. These PCs were then projected on the 769 GoNL (Genome of the Netherlands) samples (using SNP calls release 2). This figure summarizes the PC 1 versus PC 2 and the PC 1 versus PC 3 plots. Three PCs correlated significantly with geographic location and distinguished between: (1) the North and South of the Netherlands; (2) between the East and West; and (3) between the middle-band of the Netherlands and the rest of the country. When projected on the GoNL individuals, for whom we have the province of the current living address available, it is clear from the plot, that PCs capture the geographical variation in the data very well.