Genotyping

The genotyping of new samples is performed on a FinnGen ThermoFisher Axiom custom array at the Thermo Fisher genotyping service facility in San Diego.
A graph presenting the different marker categories of the genotyping array. The same information is given in the main text.
Array Content

The array consists of 736,145 probes for 655 973 markers. In addition to the core GWAS markers (about 500,000) it contains 116,402 coding variants enriched in Finland, 10,800 specific markers for the HLA/KIR region, 14,900 ClinVar variants, 4,600 pharmacogenomic variants and 57,000 selected markers that were of special interest for partners.

The marker content of the FinnGen ThermoFisher Axiom custom array v2 (current version) can be downloaded from here. The content for v1 is downloadable from here.

The legacy samples have previously been genotyped over the years using various generations of Illumina GWAS arrays. All GWAS data is imputed against a Finnish population specific whole genome sequence (WGS) backbone.