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Look-up of phenome-wide associations in GWAS catalog and with PhenoScanner v2

TL Triin Laisk
ML Maarja Lepamets
MK Mariann Koel
EA Erik Abner
RM Reedik Mägi
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FUMA v1.3.6a47 was used to compare the genome-wide significant lead signals and markers in high LD with these markers against the results in the GWAS catalog. The results of this look-up are presented in Supplementary Data 2.

PhenoScanner v248,49 was used for look-up of phenotype associations for the GWAS lead variants in previous GWAS studies. PhenoScanner query was done using the rsid-s of GWAS lead variants and the phenoscanner R package (https://github.com/phenoscanner/phenoscanner). Query results were filtered to keep one association per variant per trait, keeping studies from newer or larger studies. Descriptions of experimental factor ontology (EFO) terms and classification of EFO broad categories were obtained from the GWAS Catalog. Missing categories were added by manually searching the EMBL-EBI EFO webpage (www.ebi.ac.uk/efo/). For visualization of PhenoScanner results, parent categories with fewer results were grouped into larger categories and a heatmap was created using the pheatmap library in R 3.6.1. and a modified script from (https://github.com/LappalainenLab/spiromics-covid19-eqtl/blob/master/eqtl/summary_phenoscanner_lookup.Rmd). The results of this look-up are presented in Supplementary Data 3.

Copyright and License information: The Author(s) ©2021
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