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:

  • https://metaresults-est-ukbb.finngen.fi/
  • https://metaresults-ukbb.finngen.fi/

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