PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations
15 November 2019
Kamat MA, Blackshaw JA, Young R, Surendran P, Burgess S, Danesh J, Butterworth AS, Staley JR.
Bioinformatics (Oxford, England) (2019) 35: 22, 4851–4853
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.
Dr Praveen Surendran
Rutherford Fellow at University of Cambridge
Following undergraduate and post-graduate education in Biotechnology/Bioinformatics at Bangalore University in India and a year training as a Junior Research Fellow at the Indian Institute of...
Dr Adam Butterworth
University of Cambridge
Following training in Genetics at the University of Cambridge and Genetic Epidemiology at the University of Sheffield, Adam completed a PhD in meta-analysis of genetic association studies of...