PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations

TLDR

PhenoScanner is a curated database of publicly available results from large‑scale human genetic association studies. The paper presents a major update of PhenoScanner (V2) that expands the database to over 150 million variants and 65 billion associations across diseases, traits, gene expression, metabolites, proteins, and epigenetic markers. PhenoScanner V2 is an online tool that enables phenome scans by cross‑referencing genetic variants with many phenotypes, supports queries by genes, genomic regions, phenotypes, and variants, annotates variants with Variant Effect Predictor, maps phenotypes to Experimental Factor Ontology terms, and incorporates 1000 Genomes linkage‑disequilibrium statistics for proxy‑variant searches. PhenoScanner V2 is available at www.phenoscanner.medschl.cam.ac.uk.

Abstract

Abstract Summary PhenoScanner is a curated database of publicly available results from large-scale genetic association studies in humans. This online tool facilitates ‘phenome scans’, where genetic variants are cross-referenced for association with many phenotypes of different types. Here we present a major update of PhenoScanner (‘PhenoScanner V2’), including over 150 million genetic variants and more than 65 billion associations (compared to 350 million associations in PhenoScanner V1) with diseases and traits, gene expression, metabolite and protein levels, and epigenetic markers. The query options have been extended to include searches by genes, genomic regions and phenotypes, as well as for genetic variants. All variants are positionally annotated using the Variant Effect Predictor and the phenotypes are mapped to Experimental Factor Ontology terms. Linkage disequilibrium statistics from the 1000 Genomes project can be used to search for phenotype associations with proxy variants. Availability and implementation PhenoScanner V2 is available at www.phenoscanner.medschl.cam.ac.uk.