Genotype Arrays Used

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

Array Content

The array consists of 736,145 probes for 655,973 genetic markers. In addition to the core GWAS markers (about 500,000), the array also contains 116,402 coding variants which are enriched in Finland; 10,800 specific markers for the HLA/KIR (Human leucocyte antigen / killer cell immunoglobulin-like receptors) region; 14,900 ClinVar variants; 4,600 pharmacogenomic variants; and 57,000 selected markers that were of special interest to our 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 (below). All GWAS data is imputed against a Finnish population-specific imputation panel.

Some preference was given for testing coding variants directly on the chip vs. imputing them.

FinnGen Legacy chips

• DS1_BOTNIA_Dgi

• Affymetrix_250KNsp_250KSty

• DS2_BOTNIA_T2dgo

• lllumina_HumanOmni2.5-4v1_B_SNV_array

• DS3_COROGENE_Sanger

• Illumina Human610-Quadv1_B

• DS4_FINRISK_Corogene

• Human610-Quadv1_B

• DS5_FINRISK_Engage

• HumanCoreExome-12v1-0_A

• DS6_FINRISK_FR02_Broad

• GSAMD-24v1-0_20011747_A1

• DS7_FINRISK_FR12

• Illumina_HumanCoreExome-24-v1.1

• DS8_FINRISK_Finpcga

• Illumina_HumanCoreExome-12v1.1a

• DS9_FINRISK_Mrpred

• Illumina_HumanCoreExome-24_v1.0

• DS10_FINRISK_Palotie

• HumanCoreExome-12v1-1_A

• DS11_FINRISK_PredictCVD_COROGENE_Tarto

• HumanOmniExpress-12v1_A

• DS12_FINRISK_Summit

• HumanOmniExpress-12v1_H

• DS13_FINRISK_Bf

• Illumina_HumanCoreExome-24_v1.0

• DS14_GENERISK

• lllumina_HumanCoreExome-24v1-0_A

• DS15_H2000_Broad

• Broad_GWAS_supplemental_15061359_A1

• DS16_H2000_Fimm

• Illumina_HumanCoreExome-24v1-1_A

• DS17_H2000_Genmets

• Human610-Quadv1_B

• DS18_MIGRAINE_1

• PsychChip_15048346_B-_24

• DS19_MIGRAINE_2

• HumanCoreExome-12v1-0_A

• DS20_SUPER_1

• GSAMD-24v1-0_20011747_A1

• DS21_SUPER_2

• GSAMD-24v1-0_20011747_A1

• DS22_TWINS_1

• Illumina Human670/Human610

• DS23_TWINS_2

• IlluminaCoreExome

• DS24_SUPER_3

• GSAMD-24v1-0_20011747_A1

• DS25_BOTNIA_Regeneron

• GSA-24v1-0_A1