This repository contains tsv files that maps the Pan-UKBB GWAS results to FinnGen results.
The mapping was done using ICD-10 definitions for FinnGen endpoints. Specifically, the mapping was done using the released endpoint definitions, using columns COD_ICD_10, HD_ICD_10, and CANC_TOPO for ICD-10 definitions. The INCLUDE column was used for including other endpoint definitions to an endpoint. The match file is included in this repository.
Writeup on phenotype matching for R6: https://github.com/FINNGEN/meta-analysis-runs/tree/main/PHENOMAP_R6
Phenotype matching script: https://github.com/FINNGEN/phenotype-matching
| filename | description |
|---|---|
fg_ukbb_file |
File with matching FinnGen and Pan-ukbb endpoints, as well as google cloud storage links to summary stats of both. |
fg_R6_pan_ukbb_map.tsv |
mapping file between Finngen R6 phenotypes and the Pan-ukbb endpoints. |
fg_R8_pan_ukbb_map.tsv |
mapping file between Finngen R8 phenotypes and the Pan-ukbb endpoints. |
fg_R12_pan_ukbb_map.tsv |
mapping file between Finngen R12 phenotypes and the Pan-ukbb endpoints. |
| column | description |
|---|---|
| fg_phenotype | FinnGen phenotype name |
| fg_link | FinnGen phenotype summary statistic link. Not all of the phenotypes have been analysed, for example due to too low case numbers. |
| ukbb_phenotype | Pan-ukbb phenotype name, a Phecode or an ICD10 code. |
| ukbb_link | link to Pan-UKBB phenotype summary statistic. Lifted to build 38. |
| column | description |
|---|---|
| endpoint_1 | endpoint/phenotype that all endpoint_2s were matched against, FinnGen R6 endpoints |
| endpoint_2 | best match for endpoint_1, Pan-UKBB endpoints |
| score | similarity score between finngen(endpoint_1) and pan-ukbb (endpoint_2) endpoints calculated by dividing the size of the unique FG ICD10 codes' and unique Phecode ICD10 codes' intersection by the size of their union. |
| matches_1 | Matching ICD10 codes for FinnGen endpoint |
| matches_2 | matching ICD10 codes for Pan-UKBB endpoint |
| regex_1 | regex that was used to match FinnGen endpoint to ICD10 codes |
| regex_2 | not applicable, Pan-UKBB phenotypes were not matched using regex but a mapping from Phecodes to ICD10 |
| other_hits | All of the other pan-ukbb endpoints that matched the FinnGen endpoint. Written as 'endpoint|score' and multiple values are separated with a semicolon. |
FinnGen R12 phenotype file was acquired from FinnGen homepage and exported as tab-separated file.
Pan-ukbb phenotype file was acquired from pan-ukbb phenotype manifest
ICD10 -> phecode map was acquired from pan-ukbb github