FinnGen Handbook

Data Releases 2022

15 December 2022

  • FinnGen EA3 AMD data (version 2.0)

  • Version 2.0 of EA3 age-related macular degeneration (AMD) baseline and longitudinal files contains updated data from Tampere and Eastern Finland biobanks.

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

  • 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 data and documentation location in the Sandbox Red Library

    • /finngen/library-red/EA3_AMD_2.0/

7 December 2022

  • FinnGen R10 coding variant association results

  • The data location in the Green Library:

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

7 December 2022

  • Updated EA3_AMD_1.0 data

  • These updated EA3 age-related macular degeneration (AMD) files contain Visual acuity, Retinal thickness and anti-VEGF injection information in longitudinal format, and baseline information.

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

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

  • The data and documentation location in the Sandbox Red Library

    • /finngen/library-red/EA3_AMD_1.0/EA3_AMD_baseline_readme_1.0.txt

    • /finngen/library-red/EA3_AMD_1.0/EA3_AMD_long_readme_1.0.txt

    • /finngen/library-red/EA3_AMD_1.0/data/EA3_AMD_baseline_1.0.txt

    • /finngen/library-red/EA3_AMD_1.0/data/EA3_AMD_long_1.0.txt

1 December 2022

  • FinnGen R10 Regenie output files after step 1 (so-called nulls)

  • These files are needed to run the conditional analysis in Sandbox without the need to rerun the method from scratch.

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/finngen_R10/regenie_nulls_1.0/

  • Detailed paths to library red data from catalog:

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

24 November 2022

  • FinnGen R10 annotated bgen files

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/finngen_R10/bgen/data/annotated/

  • Detailed paths to library red data from catalog:

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

24 November 2022

  • FinnGen R10 meta-analysis results released to the Green Library

  • Data and documentation location in Google cloud:

    • FinnGen + UKBB + EstBB meta-analysis:

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

    • FinnGen + UKBB meta-analysis:

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

  • Meta-analysis browsers have been updated with the latest results:

17 November 2022

  • FinnGen R10 parental endpoint data (version 1.0)

  • These files contain parental endpoints that have been generated from cause of death register data.

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/finngen_R10/parental_endpoint_1.0/

  • Detailed paths to library red data from catalog:

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

16 November 2022

  • FinnGen R10 service sector data (version 2.0)

  • Data is described in Service Sector Data.

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/finngen_R10/service_sector_data_2.0/

  • Detailed paths to library red data from catalog:

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

15 November 2022

  • FinnGen R10 parental causes of death data (version 1.0)

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/finngen_R10/parental_causes_of_death_1.0/

  • Detailed paths to library red data from catalog:

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

15 November 2022

  • FinnGen EA3 Fatty liver disease (FLD) data (version 3.0)

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

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

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/EA3_FLD_3.0/

14 November 2022

  • FinnGen R10 kinship data (version 2.0)

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/finngen_R10/kinship_2.0/

  • Detailed paths to library red data from catalog:

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

11 November 2022

  • R10 heritabilities and genetic correlations released to the Green Library

  • Sumstats after the munging step done by ldsc are added. These sumstats can be fed directly to ldsc –rg to calculate correlations.

  • Data and documentation location in Google cloud:

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

  • Paths to sumstats in FinnGen green library are formed like

    • data/munged/finngen_[RELEASE]_[PHENO].ldsc.sumstats.gz

8 November 2022

  • FinnGen R10 imputed HLA allele genotypes

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/finngen_R10/hla_1.0/

  • Detailed paths to library red data from catalog:

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

4 November 2022

  • Proteomics data (Olink and SomaLogic)

    • The data contains the first 721 FinnGen individuals.

    • Original data received as is and one with basic QC done as specified in the readme files.

    • Readme files (readme.txt) are provided within each directory.

    • Consult the providers (Olink/ SomaLogic) documentation in original_data/ folder for details of the assays and data processing.

  • The data and documentation location in Sandbox red library:

    • SomaLogic: /finngen/library-red/EA5/proteomics/soma/first_batch/

    • Olink: FinnGen/library-red/EA5/proteomics/olink/first_batch/

2 November 2022

  • FinnGen R10 truncated endpoint file (version 1.0) released to Sandbox.

  • This file is similar to the first events endpoint file released earlier, but with small adjustments:

    • Follow-up date 31.12.2020 is used in the file. That date is the same date as the end of follow-up of death register.

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

  • See description of truncated endpoint data

  • The data and documentation location in Sandbox red library:

    • /finngen/library-red/finngen_R10/truncated_endpoint_file_1.0/

  • Detailed paths to library red data from catalog:

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

1 November 2022

  • FinnGen Release 10 GWAS, finemapping, conditional analysis, colocalization and autoreporting data released in the green library:

  • This release contains new results for:

    • Sex-specific association analysis results (under summary_stats)

    • Conditional analysis results

  • GWAS data location:

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

  • Fine-mapping data location:

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

  • Conditional analysis data location:

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

  • Autoreporting data location:

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

  • Colocalization data location:

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

  • Documentation location:

    • gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_documentation/

1 November 2022

  • FinnGen 10 HLA allele analysis results released to the green library.

  • Data location in the green library:

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

  • Documentation available at:

    • gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_documentation/finngen_R10_hla_analysis.pdf

27 October 2022

  • FinnGen R10 visual impairment register data (version 1.0) released to Sandbox.

  • Data is described on The Finnish Register of Visual Impairment page.

  • Data and documentation location in Sandbox red library

    • /finngen/library-red/finngen_R10/visual_impairment_register_1.0/

  • Detailed paths to library red data from catalog:

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

20 October 2022

  • FinnGen EA3 FLD data (version 2.0)

  • The data contain laboratory and physiological measurements from the EA3 FLD cohort

  • Data was delivered from Helsinki, Auria and Eastern Finland biobanks.

  • Number of unique FINNGENID's: 55387

  • Data and documentation location in Sandbox red library

    • /finngen/library-red/EA3_FLD_2.0/

12 October 2022

  • Finngen R10 cluster plot data

  • Cluster plots location in the GREEN library in Google cloud:

    • gs://finngen-production-library-green/finngen_R10/cluster_plots/

  • The cluster plot tsv files, that contain genotype intensities per variant for a subset of samples used in the cluster plots are released to the Sandbox at:

    • /finngen/library-red/finngen_R10/cluster_plot_1.0/data/

  • Detailed paths of this data from the manifest file:

    • /finngen/library-red/finngen_R10/cluster_plot_1.0/manifest.txt

11 October 2022

  • FinnGen R10 PRS data (version 1.0).

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/prs_1.0/

  • Detailed paths to library red data from catalog:

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

3 October 2022

  • FinnGen DF10 socioeconomic data released to the SES Sandbox.

  • The socioeconomic data of FinnGen study subjects is available to a separate Sandbox environment (SES-Sandbox) and can be accessed only by researchers in Finland The registry data and accessing proses are described in the How to apply SES sandbox access section.

  • Path to the data is the SES-Sandbox:

    • /finngen/pipelines/finngen_R10/socio_register_1.0/

3 October 2022

  • FinnGen R10 detailed version of Finnish cancer registry data (version 1.0)

  • The data contains 90303 FinnGen participants.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/cancer_detailed_1.0/

  • Detailed paths to library red data from catalog:

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

3 October 2022

  • FinnGen R10 cancer screening data (version 1.0)

  • The files contain data from Finnish nationwide breast and cervical cancer screening.

    • The breast cancer screening file contains data of 143 233 FinnGen participants.

    • The cervix cancer screening file contains data of 206 253 FinnGen participants.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/cancer_screening_1.0/

  • Detailed paths to library red data from catalog:

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

22 September 2022

  • FinnGen DF10 genotype data converted to plink format released to the Sandbox

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/genotype_plink_1.0/

  • Detailed paths to library red data from catalog:

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

19 September 2022

  • FinnGen R10 infectious disease register corona data (version 1.0)

  • The data contains 72350 (cumulative number) corona virus positive FinnGen participants.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/infectious_disease_register_corona_1.0/

  • Detailed paths to library red data from catalog:

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

19 September 2022

  • FinnGen R10 vaccination register data (version 1.0)

  • The data contains vaccination data of 385 747 FinnGen participants.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/vaccination_register_1.0/

  • Detailed paths to library red data from catalog:

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

9 September 2022

  • FinnGen DF10 reproductive history data

  • Description of the reproductive history data

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/birth_and_dvv_register_1.0/

  • Detailed paths to library red data from catalog:

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

5 September 2022

  • FinnGen DF10 datasets released to Sandbox

  • Relatedness analysis results

    • /finngen/library-red/finngen_R10/kinship_1.0/

  • PCA

    • /finngen/library-red/finngen_R10/pca_1.0/

  • Endpoints and covariates used in core DF10 analyses

    • /finngen/library-red/finngen_R10/analysis_covariates/

  • Bgen chunks for running GWAS in 40k variant chunks:

    • /finngen/library-red/finngen_R10/bgen/

  • Detailed paths to library red data from catalog:

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

29 August 2022

  • FinnGen EA3 AMD data (version 1.0)

  • These files contain diagnoses, procedures and structural form answers from AMD patients. Data was delivered to us from Helsinki biobank.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/EA3_AMD_bcb_1.0/

29 August 2022

  • FinnGen DF10 chip data (version 1.0)

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/chipd_1.0/data/

    • Markdown of all genotype QC for both chip and imputation data /finngen/library-red/finngen_R10/R10_genotype_qc.md

  • Detailed paths to library red data from catalog:

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

24 August 2022

  • FinnGen DF10 service sector data (version 1.0)

  • See the description of service sector data.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/service_sector_data_1.0/

  • Detailed paths to library red data from catalog:

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

23 August 2022

  • Please find DF10 Register of Congenital Malformations data (version 1.0)

  • The Register of Congenital Malformations is described in the FinnGen Analyst Handbook.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R10/malformation_register_1.0

  • Detailed paths to library red data from catalog:

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

15 August 2022

  • FinnGen release 10 genotype and phenotype data

  • Finngen R10 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 = 430 897

    • 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_R10/genotype_1.0/

    • Phenotypes & Documentation:

      • /finngen/library-red/finngen_R10/phenotype_1.0/

    • Detailed paths to library red data from catalog:

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

30 June 2022

  • VNR code mappings released to the Sandbox. For example, dosage and strength of drugs are mapped and available in the Sandbox and FinnGen library green.

  • Data and documentation location in Sandbox:

    • /finngen/library-green/finngen_R6/finngen_R6_medical_codes/fgVNR.tsv

    • /finngen/library-green/finngen_R6/finngen_R6_medical_codes/fgVNR_readme.txt

    • /finngen/library-green/finngen_R6/finngen_R6_medical_codes/fgVNR_table_definition.tsv

  • Data and documentation location in Google cloud:

    • gs://finngen-production-library-green/finngen_R6/finngen_R6_medical_codes

28 June 2022

  • FinnGen R9 service_sector_data_all_registers (version 1.0)

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/service_sector_data_all_registers_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

21 June 2022

  • FinnGen R9 HLA analysis results.

  • Analysis results location in Google cloud:

    • gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/hla/

  • Analysis results location in Sandbox:

    • /finngen/library-green/finngen_R9/finngen_R9_analysis_data/hla/

  • The analysis readme location in Google cloud:

    • gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_documentation/finngen_R9_hla_analysis.md

    • gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_documentation/finngen_R9_hla_analysis.pdf

  • The analysis readme location in Sandbox:

    • /finngen/library-green/finngen_R9/finngen_R9_analysis_documentation/finngen_R9_hla_analysis.md

    • /finngen/library-green/finngen_R9/finngen_R9_analysis_documentation/finngen_R9_hla_analysis.pdf

10 June 2022

  • FinnGen R9 infectious disease register corona data (version 2.0)

  • This data contains 57333 (cumulative number) corona virus positive FinnGen participants. After these 50 000 new cases over the last 6 months, almost 15 % of Finngen participants have now been tested positive for corona.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/infectious_disease_register_corona_2.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

31 May 2022

  • FinnGen R9 PRS data (version 1.0) released to Sandbox.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/prs_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

16 May 2022

  • FinnGen R9 parental causes of death (version 1.0) released to Sandbox.

  • The data is described in Other registry data files in Sandbox.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/parental_causes_of_death_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

13 May 2022

  • Results from FinnGen release 9 meta-analyses with UKBB and EstBB

  • Data and documentation location in Google cloud:

    • gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/ukbb_meta/

    • gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/ukbb_estbb_meta/

  • Data and documentation location in Sandbox:

    • /finngen/library-green/finngen_R9/finngen_R9_analysis_data/ukbb_meta/

    • /finngen/library-green/finngen_R9/finngen_R9_analysis_data/ukbb_estbb_meta/

2 May 2022

  • FinnGen R9 visual impairment register data (version 1.0)

  • The data is described in section Other registry data files in Sandbox.

  • Data and documentation location in Sandbox: /finngen/library-red/finngen_R9/visual_impairment_register_1.0/

  • Detailed paths to library red data from catalog: /finngen/library-red/finngen_R9/catalog/catalog.txt

26 April 2022

  • FinnGen R9 kidney disease register data (version 1.0)

  • The data is described in Other registry data files in Sandbox

  • Data and documentation location in Sandbox: /finngen/library-red/finngen_R9/kidney_disease_register_1.0/

  • Detailed paths to library red data from catalog: /finngen/library-red/finngen_R9/catalog/catalog.txt

14 April 2022

  • R9 coding variant analysis results have been released in green library.

  • Data location in Google cloud: gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/coding/full

  • Documentation location in Google cloud: gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/coding/R9_coding_variant_results_full.README

  • Data location in Sandbox: /finngen/library-green/finngen_R9/finngen_R9_analysis_data/coding/full

  • Documentation location in Sandbox: /finngen/library-green/finngen_R9/finngen_R9_analysis_data/coding/R9_coding_variant_results_full.README

13 April 2022

  • R9 GWAS, finemapping, colocalization and autoreporting data in green library.

  • Notable changes:

  • GWAS analysis performed for 2272 endpoints, including 3 quantitative

  • Maximum region changed from 6 MB to 10 MB in finemapping

  • Data location in Google cloud:

    • GWAS: gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/summary_stats

    • fine-mapping: gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/finemap

    • autoreporting: gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/autoreporting

    • colocalization: gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_data/colocalization

    • The documentation is available at: gs://finngen-production-library-green/finngen_R9/finngen_R9_analysis_documentation/

  • Data location in Sandbox:

    • GWAS: /finngen/library-green/finngen_R9/finngen_R9_analysis_data/summary_stats

    • fine-mapping: /finngen/library-green/finngen_R9/finngen_R9_analysis_data/finemap

    • autoreporting: /finngen/library-green/finngen_R9/finngen_R9_analysis_data/autoreporting

    • colocalization: /finngen/library-green/finngen_R9/finngen_R9_analysis_data/colocalization

    • The documentation is available at: /finngen/library-green/finngen_R9/finngen_R9_analysis_documentation/

13 April 2022

  • R8 susie finemapping version 2.0 data in green library.

  • Changes:

    • Susie version 0.11.92 used

    • individual Bayes factors for each variant added to data

  • This data does not include FINEMAP finemapping, since that has not changed since 1.0.

  • The new susie data is available at: gs://finngen-production-library-green/finngen_R8/finngen_R8_analysis_data/finemap_2.0

  • Documentation, including file descriptions, is available at :

    • Data location in Google cloud: gs://finngen-production-library-green/finngen_R8/finngen_R8_analysis_documentation/readme_r8_finemap_2.0.md

    • Data location in Sandbox: /finngen/library-green/finngen_R8/finngen_R8_analysis_documentation/readme_r8_finemap_2.0.md

11 April 2022

  • FinnGen R9 service sector data (version 1.0)

  • Data includes information from 392 374 FinnGen participants about

    • Service sectors and specialties of the Hilmo inpatient and outpatient register data

    • Service sector, contact type and profession of the primary care data

    • Reimbursement cost information of the kela drug register purchase data

  • Data is described in Other registry data files in Sandbox

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/service_sector_data_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

1 April 2022

  • FinnGen R9 truncated endpoint file (version 1.0)

    • Truncated endpoint file is similar to the first events endpoint file released earlier, but with small adjustments.

      • All registers have a common follow-up date 31.12.2019 in this file.

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

  • More information about the truncated endpoint file.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/truncated_endpoint_file_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

31 March 2022

  • FinnGen R9 cancer datasets

    • cancer_screening_1.0

      • This includes Finnish nationwide breast and cervical cancer screening data.

    • cancer_detailed_1.0

      • This is the detailed version of Finnish cancer registry data.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/cancer_screening_1.0/

    • /finngen/library-red/finngen_R9/cancer_detailed_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

17 March 2022

  • FinnGen R9 infectious disease register corona data (version 1.0)

  • The data consists of 7329 (cumulative number) corona virus positive FinnGen participants until 31st December 2021.

  • This release has been processed from the same raw data as the previous R8_3.0, but filtered with R9 genotype list.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/infectious_disease_register_corona_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

16 March 2022

  • FinnGen R9 vaccination register data (version 1.0)

  • Vaccination data of 348 982 FinnGen participants

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/vaccination_register_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

16 March 2022

  • FinnGen R9 birth and dvv register data (version 1.0)

  • The data combines information from population register (DVV) (since 1953) and medical birth register (since 1987).

  • Data from 167 920 FinnGen mother participants, and 63 742 child participants.

  • Reproductive history data is described in FinnGen Analyst Handbook section Other registry data files in Sandbox

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/birth_and_dvv_register_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

10 March 2022

  • Finngen R9 cluster plot 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_R9/cluster_plot_1.0/

  • Detailed paths to library red data from manifest:

    • /finngen/library-red/finngen_R9/cluster_plot_1.0/manifest.txt

3 March 2022 (edit: Aug 2024 - meta-analysis results with Estonian biobank are no longer available)

  • FinnGen release 8, UKBB, and Estonia Biobank meta-analysis results have been updated with 48 new meta-analysed endpoints (total 98 meta-analysed endpoints)

  • The results include summary statistics from meta-analysis (including leave-one-out results) and autoreporting results.

  • Data in green library:

    • Data location in Google cloud: gs://finngen-production-library-green/finngen_R8/finngen_R8_analysis_data/ukbb_estbb_meta/

    • Data location in Sabox:/finngen/library-green/finngen_R8/finngen_R8_analysis_data/ukbb_estbb_meta/

  • Documentation in green library:

    • Data location in Google cloud: gs://finngen-production-library-green/finngen_R8/finngen_R8_analysis_data/ukbb_estbb_meta/

    • Data location in Sabox: /finngen/library-green/finngen_R8/finngen_R8_analysis_data/ukbb_estbb_meta/

  • The Pheweb instance running with these results is updated and can be found at https://metaresults-ukbb.finngen.fi/.

18 February 2022

  • FinnGen R9 malformation register data (version 1.0)

  • The Register of Congenital Malformations contains national-level data on congenital chromosomal and structural anomalies, as well as a few other congenital anomalies like congenital hypothyroidism and teratomas, detected or suspected in stillborn and live born infants and foetuses.

  • FinnGen data consist malformation register data from 7527 FinnGen mother participants and 1992 FinnGen child participants.

  • Data is described in section Other registry data files.

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/malformation_register_1.0/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

15 February 2022

  • FinnGen R9 chip data (version 1.0)

  • Data and documentation location in Sandbox:

    • /finngen/library-red/finngen_R9/chipd_1.0/

2 February 2022

  • FinnGen release 9 genotype and phenotype data

  • Finngen R9 data was imputed using SISuV4 reference panel that contains 8,554 high coverage [25x] WGS Finnish individuals.

  • The current data statistics are:

    • Number of individuals with genotypes = 392 649

    • Number of individuals with endpoints = 392 423

    • Number of imputed variants = 20 175 454

    • Number of endpoints = 4 526

  • Data and documentation location in Sandbox:

    • Genotypes in VCF format & Documentation:

      • /finngen/library-red/finngen_R9/genotype_1.0/

    • Genotypes in PLINK format and Documentation:

      • /finngen/library-red/finngen_R9/genotype_plink_1.0

    • Phenotypes & Documentation:

      • /finngen/library-red/finngen_R9/phenotype_1.0/

    • PCA/kinship results and analysis covariates:

      • /finngen/library-red/finngen_R9/kinship_1.0/

      • /finngen/library-red/finngen_R9/pca_1.0/

      • /finngen/library-red/finngen_R9/prune_1.0/

      • /finngen/library-red/finngen_R9/analysis_covariates/

  • Detailed paths to library red data from catalog:

    • /finngen/library-red/finngen_R9/catalog/catalog.txt

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