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