Overview
What FinnGen Is
FinnGen is a large public-private partnership that has collected and analyzed genome and health data from 500,000 Finnish biobank donors to understand the genetic basis of diseases. It is now expanding into understanding the progression and biological mechanisms of diseases and provides a world-class resource for breakthroughs in disease prevention, diagnosis, and treatment. PubMed Central
Scale & Infrastructure
The latest public data release (R12) is based on the full 500,000-participant cohort — representing close to 10% of the Finnish population. This data freeze consists of over 500,000 individuals, more than 21.3 million variants, and 2,500 health endpoints. biorxiv
FinnGen includes array-based genome variant data for 520,000 individuals and sequencing data for a subset of participants. The project is expanding to generate other biological data, including metabolomics, proteomics, single-nucleus RNA and ATAC sequencing, as well as immunophenotyping data. The health register data covers over 4,500 disease endpoints. PubMed
What Makes FinnGen Unique
Two features set FinnGen apart from most other biobanks:
1. The Finnish population bottleneck. Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (MAF 0.1–5%) that survived the founding bottleneck, rather than being distributed over a large number of ultrarare variants. This dramatically improves power to detect low-frequency coding variant associations. A GWAS of 1,932 diseases identified 2,733 genome-wide significant associations at 2,496 independent loci, with fine-mapping implicating 148 coding variants, 91 of which had an allele frequency <5% in non-Finnish Europeans — 62 of which were enriched more than twofold in Finland. CamNature
2. Longitudinal health registry linkage. Combining data from different registries — including ICD-10 codes, drug prescription data, and causes of death — provides opportunities to construct reliable disease endpoints as well as novel long-term phenotypes of disease progression and therapeutic response. Registries include hospital, cancer, drug purchase, population, and cause-of-death registers, captured nationwide since 1969. nih
Genotyping & Imputation
Genome variant data from most samples was produced using a customized genotyping chip with about 700,000 markers. FinnGen then performed imputation using a reference dataset derived from Finnish whole-genome sequences encompassing approximately 8,700 individuals, yielding an inferred genome sequence allowing analysis of approximately 21 million variants per individual. nih
Open Science & Data Access
Complete results and summary statistics of the FinnGen GWAS analyses are made available publicly to the whole scientific community following a one-year embargo, with public data releases made twice a year. By May 2024, FinnGen had received more than 21,000 download requests from researchers around the world. Since June 2021, results have also been incorporated into the OpenTargets Platform and Genetics portal. Results are browsable via the PheWeb browser and downloadable from Google Cloud Storage at no cost. Cbioportal
Relevance to Gynecologic Oncology
FinnGen has become a key resource for gynecologic cancer genetics in several ways:
As a GWAS contributor: FinnGen summary statistics based on 150,658 women — including 1,264 EOC cases of any histotype — have been used in large OCAC-led ovarian cancer GWAS meta-analyses, including the most recent large-scale GWAS identifying novel HGSOC susceptibility loci. medrxiv
As a Mendelian randomization resource: FinnGen GWAS summary data for gynecologic malignancies — including cervical cancer, ovarian cancer, endometrial cancer, and vulvar cancer — are widely used in Mendelian randomization studies examining causal relationships, such as the role of immune cells in gynecologic cancer risk. Aacrjournals
Endpoint richness: Because Finland has one of the world's best-linked cancer registries going back to 1969, FinnGen's gynecologic cancer endpoints are unusually well-characterized longitudinally — capturing treatment, recurrence, and mortality data that most GWAS cohorts lack.
Finnish disease enrichment: Several conditions relevant to gynecologic oncology, including endometriosis (a known ovarian cancer risk factor) and hereditary cancer syndromes, have enriched Finnish founder variants that are particularly tractable in FinnGen.
Notes
Browse phenotypes at results.finngen.fi using ICD codes: OV=C56, uterine=C54–C55, cervical=C53. Finnish genetic isolate structure powerful for rare variant associations.