FinnGen Handbook

Data Releases 2023

21 December 2023

NordDRG extension added to FinnGen DF12 service sector data

  • /finngen/library-red/finngen_R12/service_sector_data_1.0/

08 December 2023

FinnGen EA3 ovarian cancer gene test data

  • /finngen/library-red/EA3_CANCER_OVARIAN_1.0/

07 December 2023

Updates to some FinnGen EA5 cell painting files (FGIDs-TubeIDs-Donor-IDs files)

  • /finngen/library-red/EA5/cell_painting/2023-12-07-ea5-hca-all-pbmcs.xlsx

  • /finngen/library-red/EA5/cell_painting/2023-12-07-ea5-hca-analyzed-pbmcs.xlsx

FinnGen DF12 mca 1.1

Data & documentation: /finngen/library-red/finngen_R12/mca_1.1/

30 November 2023

FinnGen DF12 Coding variant association results including CHIP EWAS

Data: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/coding

Documentation: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/coding/finngen_R12_coding.md Results also available in pheweb browser: https://results.finngen.fi/coding

23 November 2023 FinnGen DF12 LOF results:

gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/lof/ 15 November 2023

FinnGen DF12 colocalization results data: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/colocalization/ documentation: green/finngen_R12/finngen_R12_analysis_documentation/finngen_R12_colocalization.md gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_documentation/finngen_R12_colocalization.pdf

15 November 2023

FinnGen DF12 malformation register (version 1.0)

  • /finngen/library-red/finngen_R12/malformation_register_1.0/

15 November 2023 FinnGen DF12 PRS results: gs://finngen-production-library-red/finngen_R12/prs_1.0 14 November 2023 FinnGen DF12 conditional analysis and genetic correlation results: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/genetic_correlation/ gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/conditional_analysis/

08 November 2023

FinnGen DF12 HLA association analysis results

data:

gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/hla/

documentation: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_documentation/finngen_R12_hla_analysis.md gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_documentation/finngen_R12_hla_analysis.pdf

06 November 2023

FinnGen DF12 socioeconomic data (version 1.0) released to SES Sandbox

  • /finngen/pipelines/finngen_R12/socio_register_1.0/

  • For this release we have fixed some leading 0's that were previously missing.

03 November 2023

FinnGen R12 autoreporting & finemapping results

  • finemapping data: /finngen/library-green/finngen_R12/finngen_R12_analysis_data/finemap

  • autoreporting data: /finngen/library-green/finngen_R12/finngen_R12_analysis_data/autoreporting

  • documentation: /finngen/library-green/finngen_R12/finngen_R12_analysis_documentation/

02 November 2023

FinnGen EA3 FLD biopsy data

  • data: /finngen/library-red/EA3_FLD_3.0/data/EA3_FLD_biopsy_3.0.txt

  • documentation: /finngen/library-red/EA3_FLD_3.0/EA3_FLD_biopsy_readme_3.0.txt

31 October 2023

FinnGen R12 hla data

  • /finngen/library-red/finngen_R12/hla_1.0/

FinnGen R12 meta-analysis results

  • The data and documentation location in the Sandbox

  • FinnGen + UKBB + EstBB meta-analysis (400 binary and 7 progression endpoints):

    • gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/meta_analysis/ukbb_estbb/

  • FinnGen + UKBB meta-analysis (856 binary and 10 progression endpoints):

    • gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/meta_analysis/ukbb/

26 October 2023

FinnGen DF12 GWAS data

  • data: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/summary_stats

  • documentation: gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_documentation/

  • pheweb link: https://r12.finngen.fi

24 October 2023

FinnGen DF12 detailed cancer data (version 1.0)

  • /finngen/library-red/finngen_R12/cancer_detailed_1.0/

FinnGen DF12 cancer screening data (version 1.0)

  • Finnish nationwide breast and cervical cancer screening data

  • /finngen/library-red/finngen_R12/cancer_screening_1.0/

20 October 2023

FinnGen DF12 kidney disease register data (version 1.0)

  • In addition to the previously released file we have now added treatment history, incidence and prevalence files

  • /finngen/library-red/finngen_R12/kidney_disease_register_1.0/

13 October 2023

FinnGen DF12 visual impairment register data (version 1.0)

  • /finngen/library-red/finngen_R12/visual_impairment_register_1.0/

11 October 2023

Data and analysis from the third batch of Olink data combined with the previous batches, bringing the total number of processed samples with Olink to 1,990 (library-red/EA5/proteomics/olink)

pQTL, finemapping and colocalization data is available as flat files in green library (gs://finngen-production-library-green/omics/proteomics/release_2023_10_11/)

The colocalization data is also loaded into finngen pheweb browser (e.g. for a specific gene https://results.finngen.fi/gene/PCSK9 [scroll to bottom] or for a signal https://results.finngen.fi/region/E4_FH/1:54839974-55239974 ).

Somascan batches 1 and 2 was re-analyzed with harmonized pipeline and utilizing r12 genotypes (includes more samples in analysis n=924). Data can be found in respective locations (library-red/EA5/proteomics/soma/second_batchv2/) and analysis results in green libdrary (gs://finngen-production-library-green/omics/proteomics/release_2023_10_11/)

9 October 2023

FinnGen DF12 imputed genotype data (version 2.0)

  • /finngen/library-red/finngen_R12/genotype_2.0/

FinnGen DF12 plink data (version 2.0)

  • /finngen/library-red/finngen_R12/genotype_plink_2.0/

FinnGen DF12 bgen data (version 2.0)

  • /finngen/library-red/finngen_R12/bgen_2.0/

FinnGen DF12 truncated endpoint file (version 1.0)

  • /finngen/library-red/finngen_R12/truncated_endpoint_file_1.0/

Additional notes

  • FinnGen DF12 genotype data (version 1.0) has been deleted

    • /finngen/library-red/finngen_R12/genotype_1.0/

    • Please see /finngen/library-red/finngen_R12/genotype_1.0/DELETED.README

6 October 2023

FinnGen EA5 single-cell multiome data

  • /finngen/library-red/EA5/multiome/batch1_3/

28 September 2023

FinnGen EA3 women's health data - endometriosis

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

25 September 2023

FinnGen EA3 cancer data - breast, prostate and ovarian

  • /finngen/library-red/EA3_CANCER_BREAST_1.0/

  • /finngen/library-red/EA3_CANCER_PROSTATE_1.0/

  • /finngen/library-red/EA3_CANCER_OVARIAN_1.0/

FinnGen EA3 women's health data - PCOS and cervical dysplasia

  • /library-red/EA3_WOMENS_HEALTH_PCOS_1.0/

  • /finngen/library-red/EA3_WOMENS_HEALTH_CERVICAL_DYSPLASIA_1.0/

FinnGen DF12 reproductive history data (version 2.0)

  • /finngen/library-red/finngen_R12/birth_and_dvv_register_2.0/

  • Empty strings in version 1.0 have been replaced with NA

22 September 2023

21 September 2023

  • FinnGen DF12 kinship data (version 1.0)

    • /finngen/library-red/finngen_R12/kinship_1.0/

  • FinnGen DF12 pca data (version 1.0)

    • /finngen/library-red/finngen_R12/pca_1.0/

18 September 2023

8 August 2023

  • Data and analysis from the second batch of Olink data (n=813) and combined with the first, bringing the total number of processed samples with Olink to 1,534.

  • After QC and id mapping the number of individuals is 1,243.

  • Raw proteomics data of batch2 and combined batch1+2 available in Sandbox

    • finngen/library-red/EA5/proteomics/olink/second_batch/

  • pQTL summary stats and finemapping for batch 1+2 combined available in the green libary:

    • library-green/omics/proteomics/release_2023_08_08/data/Olink/Finemap/

    • library-green/omics/proteomics/release_2023_08_08/data/Olink/pQTL/

  • Colocalization of olink batch1+2 to FinnGen traits available here:

  • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/colocalization/data/fg_r11_Olink_batch1_and_2.txt.gz

  • reprocessed SomaScan data from the previous 2 batches to use harmonized with Olink batch 1+2 QC and analysis:

  • Raw data:

    • library-red/EA5/proteomics/soma/second_batch/QCd/SOMA_batch_1_2_QC_all_v2.txt

  • Analysis pqtl and finemap:

    • library-green/omics/proteomics/release_2023_08_08/data/Somascan/Finemap/

    • library-green/omics/proteomics/release_2023_08_08/data/Somascan/pQTL/

  • Coloc:

    • library-green/finngen_R11/finngen_R11_analysis_data/colocalization/data/fg_r11_Soma_v2.txt.gz

  • Readme:

    • gs://finngen-production-library-green/omics/proteomics/release_2023_08_08/readme.txt

7 July 2023

  • FinnGen DF11 Blood donor data from the Finnish Red Cross Blood Service is renamed from "FHRB_blood_donor_data_1.0" to "FRCBS_blood_donor_data_1.0"

  • Data & documentation location in the Sandbox: /finngen/library-red/finngen_R11/FRCBS_blood_donor_data_1.0/

21 July 2023

  • FinnGen EA3 immune-mediated diseases files (version 1.0) released to Sandbox.

  • The data and documentation location in the Sandbox:

    • /finngen/library-red/EA3_IMMUNE_MEDIATED_DISEASES_IBD_1.0/

    • /finngen/library-red/EA3_IMMUNE_MEDIATED_DISEASES_RHEUMA_1.0/\

22 June 2023

  • FinnGen Release 11 coding variant association results and documentation

  • The data and documentation location in the Green Library

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/coding/

22 June 2023

  • FinnGen Release 11 meta-analysis results

  • The data and documentation location in the Sandbox

  • FinnGen + UKBB + EstBB meta-analysis (247 endpoints):

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/meta_analysis/ukbb_estbb/

  • FinnGen + UKBB meta-analysis (762 endpoints):

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/meta_analysis/ukbb/

2 June 2023

22 May 2023

  • FinnGen R11 parental causes of death and parental endpoints data(version 1.0)

  • The data and documentation location in the Sandbox

    • /finngen/library-red/finngen_R11/parental_endpoint_1.0/

    • /finngen/library-red/finngen_R11/parental_causes_of_death_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

19 May 2023

  • FinnGen R11 HLA analysis results

  • The data and documentation location in the green library:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/hla/

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_documentation/finngen_R11_hla_analysis.md

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_documentation/finngen_R11_hla_analysis.pdf

15 May 2023

  • FinnGen Release 11 heritability and genetic correlation analysis outputs

  • The data and documentation location in the green library:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/ldsc/

9 May 2023

  • FinnGen Release 11 GWAS, finemapping, conditional analysis, colocalization and autoreporting data

  • The data and documentation location in the green library:

  • GWAS:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/summary_stats

  • Fine-mapping:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/finemap

  • Conditional analysis:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/conditional_analysis

  • Autoreporting:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/autoreporting

  • Colocalization:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/colocalization

  • Documentation available at:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_documentation/

28 April 2023

  • FinnGen DF11 dental data (version 1.0)

  • This data is from the primary outpatient register and includes information for instance on missing and decayed teeth. A Handbook page describing this new data will be added by the end of May.

  • The data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/dental_data_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

27 April 2023

  • FinnGen DF11 visual impairment register data (version 1.0)

  • The data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/visual_impairment_register_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

27 April 2023

  • FinnGen DF11 kidney disease register data (version 1.0)

  • The data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/kidney_disease_register_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

25 April 2023

13 April 2023

  • FinnGen R11 PRS data (version 1.0)

  • The data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/prs_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

3 April 2023

  • FinnGen R11 truncated endpoint data (version 1.0)

  • Small adjustments compared to the earlier version:

    • Follow-up date 31st December 2020 is used in the file that is also the end of follow-up in death register

    • FU_END_AGEs of the individuals have been re-calculated using the updated follow-up end date.

  • The data and documentation location in Sandbox:

    • gs://finngen-production-library-red/finngen_R11/phenotype_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

27 March 2023

  • FinnGen DF11 Genetic relationship matrix and bgen files

  • The data location in Sandbox red library:

    • /finngen/library-red/finngen_R11/grm_1.0/

    • /finngen/library-red/finngen_R11/bgen/

24 March 2023

  • FinnGen DF11 cancer screening data

  • The breast cancer screening file contains data of 159 099 FinnGen participants

  • The cervix cancer screening file contains data of 230 411 FinnGen participants

  • The data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/cancer_screening_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

23 March 2023

  • FinnGen DF11 genotype data (in plink format)

  • The data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/genotype_plink_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt\

23 March 2023

  • FinnGen DF11 pca and kinship data

  • The data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/pca_1.0/

    • /finngen/library-red/finngen_R11/kinship_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

23 March 2023

  • DF11 detailed cancer data (version 1.0)

  • The detailed version of Finnish cancer registry file contains data of 111383 FinnGen participants.

  • The data and documentation location in Sandbox

    • /finngen/library-red/finngen_R11/cancer_detailed_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

17 March 2023

  • FinnGen DF11 vaccination register data

  • Vaccination data of 427 570 FinnGen participants

  • Data is described in Finnish National Vaccination Registry

  • The data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/vaccination_register_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

15 March 2023

  • pQTL analysis and finemapping results

    • 828 and 619 samples from SomaLogic and Olink respectively samples

    • Data location in the green library:

      • gs://finngen-production-library-green/omics/proteomics/release_2023_03_02/

  • Colocalization between pQTLs and all genome wide significant hits in R10 .

14 March 2023

  • FinnGen R11 HLA genotype data

  • The data contains the genotype files and the dosage files from which the genotype files were produced.

  • Data location in Sandbox:

    • /finngen/library-red/finngen_R11/hla/

  • Readme file location in Sandbox:

    • /finngen/library-red/finngen_R11/hla/finngen_R11_hla_data.pdf.

3 March 2023

  • FinnGen DF11 reproductive history data

  • Data is described in the Reproductive history data

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/birth_and_dvv_register_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

28 February 2023 (edit: Aug 2024 - meta-analysis results with Estonian biobank are no longer available)

  • FinnGen release 10 meta-analyses with Estonia biobank and UKBB

  • For more information, see Meta-analyses

  • Updated to a total of 248 endpoints

  • Data location in the Green Library:

    • gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/meta_analysis/

  • Meta-analysis browser has been updated with the latest results:

28 February 2023

  • FinnGen R11 mca (mosaic chromosomal alterations) data(version 1.0) released to Sandbox.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/mca_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

27 February 2023

  • FinnGen EA3 diabetes and rare kidney diseases v 1.0 data released to Sandbox.

  • Laboratory measurements for diabetes and rare kidney diseases.

  • Number of individuals = 16 922

  • Data have been collected from Auria Biobank, Borealis Biobank, Central Finland Biobank and Helsinki Biobank.

  • EA3 data is to be used only as stated in the respective EA3 study plan and need an accepted Analysis proposal as in all FinnGen studies.

  • The EA3 data usage is restricted to the EA3 projects. See Diabetes/RKD project documentation from the Members Area.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/EA3_DIAB_1.0/

27 February 2023

  • Finngen R11 cluster plot data

  • These data files contain genotype intensities per variant for a subset of samples that are used in cluster plots (released in the green library).

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/cluster_plot_1.0/

  • Detailed paths to library red data from manifest:

    • /finngen/library-red/finngen_R11/cluster_plot_1.0/manifest.txt

22 February 2023

  • FinnGen DF11 malformation registry data

  • Data is described in The Register of Congenital Malformations

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/malformation_register_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R11/catalog/catalog.txt

22 February 2023

  • FinnGen DF11 service sector data

  • Data is described in Service Sector Data

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R11/service_sector_data_1.0/

Figure. Upset plot showing number of shared individuals in R11 phenotype files.

14 February 2023

  • FinnGen release 11 genotype and phenotype data

  • Finngen R11 data was imputed using SISuV4.2 reference panel that contains 8,554 high coverage [25x] WGS Finnish individuals.

  • The current data statistics are:

    • Number of individuals with genotypes = 473,681

    • Number of individuals with endpoints = 429 209

    • Number of imputed variants = 21 311 942

    • Number of endpoints = 4 519

  • Data and documentation location in Sandbox:

    • Genotypes in VCF format & Documentation:

      • /finngen/library-red/finngen_R11/genotype_1.0/

    • Phenotypes & Documentation:

      • /finngen/library-red/finngen_R11/phenotype_1.0/

    • Detailed paths to library red data from catalog:

      • /finngen/library-red/finngen_R11/catalog/catalog.txt

31 January 2023

  • Proteomics data from SomaScan

  • The data contains 243 FinnGen samples. Combined with the data from the first SomaScan batch of 628 QC passing samples, the total SomaScan sample size after QC is 854.

  • See readme.txt provided within each directory. We provide original data received as is and one with basic QC done as specified in the readme files. Consult the providers (documentation in original_data/ folder) for details of the assays and data processing.

  • Data location in the Sandbox red library:

    • library-red/EA5/proteomics/soma/second_batch/

31 January 2023

  • FinnGen R10 mca data (version 1.0)

  • Data and documentation location in the Sandbox red library:

    • /finngen/library-red/finngen_R10/mca_1.0/

  • Detailed paths to library red data from the catalog:

    • /finngen/library-red/finngen_R10/catalog/catalog.txt

30 January 2023

  • FinnGen R10 mca data (version 1.0)

  • The data and documentation locations in the Sandbox red library:

    • /finngen/library-red/finngen_R10/mca_1.0/

  • See detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R10/catalog/catalog.txt

18 January 2023

  • FinnGen EA6 COG data (version 1.0)

  • EA6 Cognitive Decline in Prodromal Alzheimer's (COG) pilot data released to Sandbox.

  • See COD project documentation from the Members Area.

  • The data and documentation locations in the Sandbox Red Library

    • /finngen/library-red/EA6_COG_1.0/

18 January 2023

  • SISuv4.2 LDstore correlation (BCOR) files

  • The data location in the Green Library:

    • gs://finngen-production-library-green/imputation_panel/v4.2/LD/

  • More details in readme file:

    • gs://finngen-production-library-green/imputation_panel/v4.2/LD/README.md

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