What’s new in DF8 endpoints

For DF8 the number of endpoints was reduced. This was done for a number of reasons - partly to reduce computational costs and also because nearly redundant endpoints could be confusing.

Endpoints were reduced through careful calculation of the case overlaps and consultation with the FinnGen clinical groups.

Endpoints categorized into core and non-core endpoints

Core endpoints

• A FinnGen core endpoint is an endpoint for which GWAS analysis is run by FinnGen Analysis team. The results are shared in FinnGen Google Cloud storage green bucket and one can browse them with PheWeb.

Non-core endpoint

• Non-core endpoints are omitted from GWAS analyses, but FinnGen study subjects are still assigned into these phenotypic endpoints by Endpointter. The endpoint definitions can still be browsed in Risteys and study subjects assigned to these can be accessed in Sandbox. One can use them eg. in Custom GWAS runs in Sandbox.

Endpoints are categorized to core and non-core endpoints using the OMIT indicator (column D in endpoint Spreadsheets (https://www.finngen.fi/en/researchers/clinical-endpoints). See below what type of endpoints were considered as non-core endpoints and therefore omitted from DF8 GWAS runs. In general and all endpoints with n < 80 cases are excluded from GWAS runs.

What kind of endpoints were omitted from DF8 GWAS analyses

• Reduntant ICD-10 codes:

  • R18 Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified

  • ST19 Injury, poisoning and certain other consequences of external causes

  • VWXY20 External causes of morbidity and mortality

  • Z21 Factors influencing health status and contact with health services

  • U22 Codes for special purpose

  • Level 1 endpoints (broad upper categories, ie AB1_INFECTIONS)

• Correlated endpoints

  • Correlation runs on DF7

    • Correlated endpoints assigned to clusters

    • Top endpoint retained within each cluster

  • Clinical evaluation of “top endpoints”

• Systematic control selection for cancer endpoints

  • EXALLC version selected for malignant cancers (C3_)

  • EXALLC version omitted for benign cancers (CD2_BENIGN_)

All FinnGen core and non-core endpoints can be found at FinnGen web pages.

• Spreadsheet: FINNGEN_CORE_AND_NONCORE_ENDPOINTS_AND_CONTROLS_DF8