Data Releases 2025

June 10

FinnGen DF13 imputed HLA genotypes

• Data: /finngen/library-red/finngen_R13/hla_1.0/

• Documentation: /finngen/library-red/finngen_R13/hla_1.0/finngen_R13_hla_data.pdf

May 31

FinnGen DF13 GWAS

• Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/summary_stats/

• Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_analysis_document_GWAS.pdf

FinnGen DF13 Fine-mapping

• Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/finemap/

• Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_finemap.md

FinnGen DF13 Autoreporting

• Data: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_data/autoreporting/

• Documentation: gs://finngen-production-library-green/finngen_R13/finngen_R13_analysis_documentation/finngen_R13_autoreporting.md

May 7

THL Super Olink Proteomics data

This is a small plasma proteomics dataset (with Olink Explore HT, ~5.3K proteins) from (n=92) SUPER study participants. The SUPER study focuses on the progression of psychotic disorders, and the individuals for whom we analyzed their proteomics were selected because they are carrying certain rare variants associated with psychotic disorders. For additional information on this dataset, please contact Olli Pietiläinen ([e-mail]).

• /finngen/library-red/omics/proteomics/THL_SUPER/

April 22

FinnGen DF13 truncated endpoint file

• /finngen/library-red/finngen_R13/truncated_endpoint_file_1.0/

FinnGen DF13 parental data

• /finngen/library-red/finngen_R13/parental_causes_of_death_1.0/

• /finngen/library-red/finngen_R13/parental_endpoint_1.0/

April 10

FinnGen DF13 analysis covariates Analysis covariates are tab-separated gzip-compressed files that contain covariate and endpoint data for each sample.

/finngen/library-red/finngen_R13/analysis_covariates/

FinnGen DF13 GRM data GRM contains a high-quality LD-pruned subset of the imputed genotypes in Plink bed-format.

• /finngen/library-red/finngen_R13/grm_1.0/

FinnGen DF12 OMICSPRED PGS models released to Sandbox.

FinnGen PGS Browser Data Release R12 Notes Note: The current release only includes proteomics models from OmicsPred. All data are derived from OmicsPred, based on three datasets: UKBB (EUR), n=2,312 INTERVAL, n=273 Somalogic, n=1,645

More information in the provided readme

• /finngen/library-red/finngen_R12/pgs_browser_db_1.0/

April 8

DF13 cancer screening data (breast and cervical)

• /finngen/library-red/finngen_R13/cancer_screening_1.0/

April 4

DF13 detailed cancer data

• /finngen/library-red/finngen_R13/cancer_detailed_1.0/

DF13 Extended Hilmo and Avohilmo data

• /finngen/library-red/finngen_R13/hilmo_avohilmo_extended_1.0/

March 22

Genotype bgen/plink /finngen/library-red/finngen_R13/plink_1.0/ /finngen/library-red/finngen_R13/bgen_1.0/ PCA: /finngen/library-red/finngen_R13/pca_1.0/ PCA inliers (unrelated finns) : 281515 PCA outliers (related finns) : 218975 PCA rejected (non finns and duplicates) : 19482 PCA final samples : 500490 KINSHIP: /finngen/library-red/finngen_R13/kinship_1.0/

March 21

R13 visual impairment register data

/finngen/library-red/finngen_R13/visual_impairment_register_1.0/

March 20

R13 Kanta lab & analysis data: /finngen/library-red/finngen_R13/kanta_lab_1.0/ /finngen/library-red/finngen_R13/kanta_analysis_1.0/ March 17

FinnGen R13 service sector data(version 1.0) released to Sandbox .

/finngen/library-red/finngen_R13/service_sector_data_1.0/

March 10

Kanta lab value analysis v2 of 388 labs. Main changes are that all lab values are now inverse rank normalised to make comparisons/meta-analyses easier. Additionally certain derived lab values are also analysed (e.g. non-HDL cholesterol, EGFR computed from creatinine). N samples for many binary tests(mostly antibody tests) is increased by not only using result text (positive/abnormal/high) but including manually curated thresholding of lab values. Find below description of the analyses and metadata of all lab values analysed. Browser at kanta.finngen.fi is updated to display these new results. Find flat files of the results in green library gs://finngen-production-library-green/lab_values/gwas_release_2025_3_10/

Find the lab value phenotype file used in the analysis in red library (library-red/finngen_R12/analysis_covariates/kanta_lab_v2analysis_data_2025_3_10.txt.gz)

42KB

FinnGen_kanta_lab_documentation_v2.pdf

pdf

46KB

Kanta_labs_GWAS_results_v2_summary.xlsx

5 March

FinnGen DF13 genotypes and phenotypes released to Sandbox red library.

The current data statistics are: Number of individuals with genotypes = 519,972 Number of individuals with endpoints = 519,972 Number of imputed variants = 21,331,644 Number of endpoints = 4,662

You can find the data and documentation in Sandbox red library:

Genotypes in VCF format & Documentation: /finngen/library-red/finngen_R13/genotype_1.0/

Phenotypes & Documentation: /finngen/library-red/finngen_R13/phenotype_1.0/

The lower number of individuals in this release compared to release 12 is due to excluding new sample denials. However, the registry data is updated from R12 for all individuals.

28th February

FinnGen 3 QCd Olink proteomics dataset of 2094 individuals.

protein expression data:

library-red/omics/proteomics/olink_genewiz_batch1_QCd_2025_28_02/

pQTL and finemap in 1,829 independent samples of the above:

gs://finngen-production-library-green/omics/proteomics/olink_genewiz_batch1_QCd_2025_28_02/

13 February

FinnGen EA5 PBMC metadata files released to Sandbox. This file includes timestamp information for all PBMC samples FRC Blood Service Biobank has delivered to FinnGen between 2021-2024. More information is available in the provided readme.

• /finngen/library-red/ EA5/omics_metadata/20250130_EA5_PBMCs_Metadata_All.csv

• /finngen/library-red/ EA5/omics_metadata/20250204_EA5_PBMC_Metadata_Readme.md

5 February

FinnGen EA5 plasma metadata files released to Sandbox. This file includes timestamp information for all plasma samples FRC Blood Service Biobank has delivered to FinnGen between 2021-2024. More information is available in the provided readme.

• /finngen/library-red/ EA5/omics_metadata/20250204_EA5_Plasma_Metadata_All.csv

• /finngen/library-red/EA5/omics_metadata/20250204_EA5_Plasma_Metadata_Readme.md

9 January

FinnGen EA3 endometriosis data was supplemented by pain related text mining data, ICD-10 data and Nordic classification of surgical procedures (NCSP) data. ICD-10 and NCSP codes have been used for selecting cohort for endometriosis related pain. EA3 endometriosis medication data was released to Sandbox earlier.

• /finngen/library-red/EA3_WOMENS_HEALTH_ENDOMETRIOSIS_1.0/