Concepedia

PhenoScanner: a database of human genotype–phenotype associations

James R Staley, James Blackshaw, Mihir Kamat, Praveen Surendran, Benjamin B. Sun, Dirk S. Paul, Daniel Freitag, Stephen Burgess, John Danesh, Robin Young,

Bioinformatics · 2016 · 1.6K citations · 8 references

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TL;DR

PhenoScanner is a curated database of publicly available results from large‑scale genetic association studies. The tool facilitates phenome scans by cross‑referencing genetic variants with many phenotypes to aid understanding of disease pathways and biology. The database contains over 350 million association results for more than 10 million unique SNPs and is accessed via a web interface that allows queries by variant, allele‑aligned results, and proxy searches using European 1000 Genomes and HapMap data. PhenoScanner is available at www.phenoscanner.medschl.cam.ac.uk (contact jrs95@medschl.cam.ac.uk); supplementary data are available online.

Abstract

Abstract Summary: PhenoScanner is a curated database of publicly available results from large-scale genetic association studies. This tool aims to facilitate ‘phenome scans’, the cross-referencing of genetic variants with many phenotypes, to help aid understanding of disease pathways and biology. The database currently contains over 350 million association results and over 10 million unique genetic variants, mostly single nucleotide polymorphisms. It is accompanied by a web-based tool that queries the database for associations with user-specified variants, providing results according to the same effect and non-effect alleles for each input variant. The tool provides the option of searching for trait associations with proxies of the input variants, calculated using the European samples from 1000 Genomes and Hapmap. Availability and Implementation: PhenoScanner is available at www.phenoscanner.medschl.cam.ac.uk. Contact: jrs95@medschl.cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.