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R4
R4
  • Introduction
  • Data download
  • Data description
  • Data releases
  • How to cite
  • Methods
    • Participating biobanks/cohorts
    • Genotypes
      • Genotype data
      • Genotype imputation
      • SISu reference panel
      • Software used
      • LD estimation
    • Endpoints
    • GWAS
      • Sample QC and PCA
      • Association tests
    • Fine-mapping
    • Contact
    • Github
    • FinnGen
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  1. Methods

Endpoints

PreviousLD estimationNextGWAS

Last updated 4 years ago

CtrlK
  • Registries
  • Excluded endpoints
  • Risteys

Registries

The disease endpoints were defined using nationwide registries:

  • Drug purchase and Drug Reimbursement

  • Digital and Population Data Services Agency

  • Statistics Finland

  • Register of primary health care visits: AVOHILMO

  • Care Register for Health Care: HILMO

  • Finnish cancer registry

We harmonized over the International Classification of Diseases (ICD) revisions 8, 9 and 10, cancer-specific ICD-O-3, (NOMESCO) procedure codes, Finnish-specific Social Insurance Institute (KELA) drug reimbursement codes and ATC-codes.

These registries spanning decades were electronically linked to the cohort baseline data using the unique national personal identification numbers assigned to all Finnish citizens and residents.

A full list of FinnGen endpoints is available online for release 4.

Excluded endpoints

The endpoints with fewer than 100 cases, near-duplicate endpoints, and developmental “helper” endpoints were excluded from the final PheWas (column “OMIT”).

Endpoints with N<150 are not released by THL (Finnish Institute for Health and Welfare).

Risteys

risteys.finngen.fi (Risteys = intersection in Finnish) allows browsing of the FinnGen data at the phenotype level, including endpoint definitions, statistics about number of individuals, gender distribution, and longitudinal relationships.