The genotyping of new samples is performed on a FinnGen ThermoFisher Axiom custom array at the Thermo Fisher genotyping service facility in San Diego.
Pipetting robot in action.
Pipetting robot

The current array (v2) contains 723,376 probesets for 664,510 markers. In addition to the core GWAS markers (about 500,000) it contains about 116,000 coding variants enriched in Finland, >10,000 specific markers for the HLA/KIR region, almost 15 000 ClinVar variants, about 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 (657,675 markers) 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.

Test file.