PRSComp Disease/trait database

The Disease/trait database is constructed based on GWAS Catalog summary statistics data of genetic risk score of diseases and traits accessed in June 2022 [13]. GWAS Catalog records were curated to fulfill the following criteria: biallelic single nucleotide variant, SNP containing information on effect size, genotyped at 1KG3 and HGDP (see Reference genotyped dataset) and not ambiguous. From them, SNP with conditional effect were excluded. A threshold of P-value lower than 1x10-8 for the associated SNP was also established. In addition, OR values were transformed to their corresponding ln(OR) and SNPs were coded by their risk allele.
The curated set of GWAS Catalog records were grouped into a set of query entries by using GWAS Catalog fields: “DISEASE/TRAIT”, “MAPPED_TRAIT”, “STUDY ACCESSION”, ancestry population and the unit measure of the SNP effect, extracted from “95% CI(TEXT)” field to describe a specific disease/trait study. Each query entry was then assigned to one of these main categories: Cancer/Neoplasm (514 entries, 2,211 SNPs), Disorder/Diseases (2,320 entries, 18,085 SNPs), Processes/measurements (7,037 entries, 52,337 SNPs) and Trait/conditions (203 entries, 2,423 SNPs). Then, each category was subdivided into additional subcategories according to the “Experimental Factor Ontology” field assigned at GWAS Catalog and complemented by querying the Open Targets Platform to refine the phenotype under study if necessary.
We have incorporated the GWASROC-ID (https://gwasrocs.ca) to those PRScomp entries included in the GWASROC database (matching at PUBMEDID and rsID).