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

Kamat, M. A., Blackshaw, J. A., Young, R. , Surendran, P., Burgess, S., Danesh, J., Butterworth, A. S. and Staley, J. R. (2019) PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations. Bioinformatics, 35(22), pp. 4851-4853. (doi: 10.1093/bioinformatics/btz469) (PMID:31233103) (PMCID:PMC6853652)

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Abstract

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.

Item Type:Articles
Additional Information:This work was supported by the UK Medical Research Council [G0800270, MR/L003120/1]; the British Heart Foundation [SP/09/002, RG/13/13/30194, RG/18/13/33946]; Pfizer [G73632]; the European Research Council [268834]; the European Commission Framework Programme 7 [HEALTH-F2-2012-279233]; the National Institute for Health Research; and Health Data Research UK.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Young, Dr Robin
Authors: Kamat, M. A., Blackshaw, J. A., Young, R., Surendran, P., Burgess, S., Danesh, J., Butterworth, A. S., and Staley, J. R.
College/School:College of Medical Veterinary and Life Sciences > Institute of Health and Wellbeing > Robertson Centre
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:24 June 2019
Copyright Holders:Copyright © 2019 The Authors
First Published:First published in Bioinformatics 35(22):4851–4853
Publisher Policy:Reproduced under a Creative Commons License

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