# Data Releases 2024 **31 December** The first FinnGen 3 Olink Explore HT (5.3k proteins) data of 2,135 samples in sandbox (library-red/omics/proteomics/olink\_genewiz\_batch1\_31\_12\_24/). See readme.txt within for release notes of different data files. Note that the data provided at this point is original data from our Olink provider GeneWiz without any additional quality control applied. It is not recommended to use the data without first performing appropriate quality control as needed for your analysis. You can expect fully quality controlled data by the FinnGen core team in Jan/Feb 2025. **20 December** FinnGen [IBD task force snomed data](https://docs.finngen.fi/finngen-data-specifics/disease-specific-task-force-data/inflammatory-bowel-disease-ibd-snomed-codes-data) released to Sandbox. This data contains pathology biopsy related snomed diagnosis codes from IBD patients in FinnGen. * /finngen/library-red/task\_force\_data/IBD/ **17 December** Kanta prescription data (version 1.0) released to red library: * /finngen/library-red/finngen\_R12/kanta\_prescription\_1.0/ **10 December 2024** First set of Kanta lab value association results, including GWAS, finemap, autoreporting, and ldsc (heritability and genetic correlations) results: * /finngen/library-green/lab\_values/gwas\_release\_2024\_12\_1/ **5 December 2024** Additional EA3 Women's health PCOS data set added (detailed phenotypes from infertility variant carriers) **2 December 2024** Pilot set of Hospital administered medication released to Sandbox. This pilost set consists of 25 drugs and data is from Helsinki and Central Finland biobanks. * /finngen/library-red/Hospital\_Administered\_Medications **12 November 2024** Released a version of FinnGen R8 regenie nulls in order to be able to run conditional analysis for R8. * /finngen/library-red/finngen\_R8/analysis\_null\_models/ **19 September 2024** A version of the R12 analysis phenotype-covariate file is released in sandbox. This version only has analysis phenotypes in it, without covariates. * File location: /finngen/library-red/finngen\_R12/analysis\_covariates/R12\_PHENO\_V2.FID.txt.gz **10 September 2024** A new release of R12 cluster plots in sandbox. The version 2.0 cluster plots include some missing variants from previous releases. Also, the sampling schema has been updated to better preserve imputed call outliers. * Cluster plots: /finngen/library-green/finngen\_R12/cluster\_plots\_v2/ * Cluster plot data files: /finngen/library-red/finngen\_R12/cluster\_plot\_2.0/ * Readme: /finngen-library-red/finngen\_R12/cluster\_plot\_2.0/finngen\_R12\_cluster\_plot\_2.0\_readme.txt **30 August 2024** An additional file released to FinnGen [EA3 Heart Failure](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-heart-failure-variables) data. \ Specifically, this is an extra ejection fraction data file that contains measurements that previously had missing dates and have now been constructed. * /finngen/library-red/EA3\_HEART\_FAILURE\_1.0/ **29 August 2024** FinnGen R12 Kanta lab values data. `/finngen/library-red/finngen_R12/kanta_1.0/` **20 June 2024** FinnGen R12 [recessive GWAS](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/recessive-gwas-results-format) results. * Data: gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/summary\_stats\_recessive/results * Documentation: gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_documentation/finngen\_R12\_recessive\_gwas.md **30 May 2024** [FinnGen EA3 Women's health data](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-womens-health-studies) - [cervical dysplasia](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-womens-health-studies/ea3-womens-health-human-papilloma-virus-related-gynecological-lesions-study-and-data) files (version 2.0). In this version Tampere biobank participants were added to data. * /finngen/library-red/EA3\_WOMENS\_HEALTH\_CERVICAL\_DYSPLASIA\_2.0/ **6 May 2024** FinnGen R12 sex-specific GWAS results and meta-analysis results (for combined and heterogeneity). Individual female- and male-specific results for 2,207 FinnGen R12 endpoints (262 endpoints missing due to being unsuitable for these analyses) and a set of meta-analysed files that contain both female and male associations, and heterogeneity of effect between sexes. Also single file containing meta-analysis statistics across all endpoints for variants reaching genome-wide significance (P<=5E-8) in either sex. Female- and male-specific REGENIE GWA summary statistics: * gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/sex\_difference/summary\_stats/ Meta-analysed summary files with heterogeneity statistics: * gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/sex\_difference/meta\_analysis/meta\_summary\_stats/ Statistics of variants reaching genome-wide significance in either sex (all endpoints in same file): * gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/sex\_difference/meta\_analysis/sex\_specific\_meta\_gwsig\_in\_either\_sex\_all\_endpoints.tsv.gz List of excluded endpoints (with their exclusion reason): * gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/sex\_difference/regenie\_single\_sex\_drop\_list\_plus\_reason\_262\_endpoints.txt **8 April 2024** FinnGen EA3 OCT data (of [EA3 AMD](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-age-related-macular-degeneration-project-and-data-in-sandbox) project) and ECG data (of [EA3 Heart Failure](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-heart-failure-variables) project) These are pilot data sets for new data types planned for FinnGen 3. Optical coherence tomography (OCT) images for AMD patients are acquired from Eastern Finland Biobank. Data set contains longitudinal OCT images and corresponding dates. ECG pilot data is from Cental Finland biobank and contains longitudinal ECGs from all individuals from whom ECG has been taken. * /finngen/library-red/EA3\_AMD\_2.0/ * /finngen/library-red/EA3\_HEART\_FAILURE\_1.0/ **13 March 2024** FinnGen NMR data NMR data of FinnGen samples provided to THL from Nightingale which is now released to the FinnGen Sandbox for analysis. This data contains 46,556 samples from the following THL BIOBANK cohorts: DILGOM2007 n= 4539\ DILGOM2014 n= 1186\ FINRISK1997 n= 7095\ FINRISK2002 n= 6968\ FINRISK2007 n= 5299\ FINRISK2012 n= 5440\ FinHealth17 n= 5165\ Health2000 n= 6574\ Health2011 n= 4290 Number of samples: (46556)\ Number of unique FinnGen IDs: (37245)\ Number of FinnGen IDs that occur more than once: (8149)\ Number of NMR variables: (between 330 and 494) There are 330-494 NMR variables which are further described in Variable\_description \*.csv files All data has been consistently analyzed by Nightingale with their latest software and is described in detail in the manuscript available at Note that many of the samples are taken on the same individuals at different time points (e.g., Health2011 is a followup of Health2000, and DILGOM2014 is likewise followup of DILGOM2007 (a subset of FINRISK2007) - in total there are 8,149 repeated samples. Hence the sample size for genetic association is more on the order of 35,000 but there are very valuable longitudinal analyses possible. * /finngen/library-red/nmr/ **28 February 2024** FinnGen WES gnomAD v4 vcf files This data release contains 25,201 samples in total from the FINRISK (n=12203), Health2000 (n=4618) and SUPER (n=8380) collections. The sample is highly enriched for psychosis patients (the entire SUPER cohort) and subsets of FINRISK were selected as part of Alzheimer's and IBD sequencing projects. These data were extracted from the gnomAD v4 exome callset generated at the Broad Institute and have not gone through additional QC after the gnomAD calling. * /finngen/library-red/wes\_gnomad\_v4\_no\_qc/ **20 February 2024** FinnGen WGS Gnomad v3 vcf files.\ This data contains 2,463 samples from FINRISK, H2000, Migraine and SUPER cohorts. \ The data has not gone through any QC. * /finngen/library-red/wgs\_gnomad\_v3\_no\_qc/ **9 February 2024** Pathology data of FinnGen [EA3 Oncology - Ovarian Cancer](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-oncology-studies/ea3-study-ovarian-cancer-study-variables) project * /finngen/library-red/EA3\_CANCER\_OVARIAN\_1.0/ FinnGen WGS SISu v4 vcf files.\ This data contains 3,237 FINRISK samples and has not gone through any QC. * /finngen/library-red/wgs\_sisu\_v4\_no\_qc/ **7 February 2024**\ \ FinnGen [Genetic Ancestry](https://docs.finngen.fi/finngen-data-specifics/red-library-data-individual-level-data/genotype-data/types-of-genotype-files-available/genetic-ancestry) data * /finngen/library-red/finngen\_R12/genetic\_ancestry\_1.0
**1 February 2024** FinnGen [EA3 prostate cancer](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-oncology-studies/ea3-study-prostate-cancer-study-variables) pathology data * /finngen/library-red/EA3\_CANCER\_PROSTATE\_1.0/ **17 January 2024** Added data for physiological measurements for [EA3 Women's health PCOS](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-womens-health-studies/ea3-study-womens-health-female-infertility-and-pcos-study-variables) project * /finngen/library-red/EA3\_WOMENS\_HEALTH\_PCOS\_1.0/ **16 January 2024** Updated version of FinnGen DF12 [mosaic chromosomal alterations](https://docs.finngen.fi/finngen-data-specifics/red-library-data-individual-level-data/genotype-data/types-of-genotype-files-available/mca-data) data. \ The main change is that the previous release (mca\_1.1) used SHAPEIT5 for phasing while the updated release (mca\_2.1) changed back to SHAPEIT4. * /finngen/library-red/finngen\_R12/mca\_2.1/ **10 January 2024** Added age group information for FinnGen [EA3 Women's health PCOS](https://docs.finngen.fi/finngen-data-specifics/expansion-area-3-ea3-projects/ea3-study-womens-health-studies/ea3-study-womens-health-female-infertility-and-pcos-study-variables) project * /finngen/library-red/EA3\_WOMENS\_HEALTH\_PCOS\_1.0/