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

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Kamat, Mihir A 
Blackshaw, James A 
Young, Robin 

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.

Description

Keywords

Genetic Association Studies, Genome, Genome-Wide Association Study, Genotype, Humans, Linkage Disequilibrium, Phenotype, Polymorphism, Single Nucleotide, Software

Journal Title

Bioinformatics

Conference Name

Journal ISSN

1367-4803
1367-4811

Volume Title

35

Publisher

Oxford University Press (OUP)

Rights

All rights reserved
Sponsorship
Medical Research Council (G0800270)
European Research Council (268834)
Medical Research Council (MR/L003120/1)
British Heart Foundation (None)
Medical Research Council (MR/S003746/1)
Medical Research Council (MC_UU_00002/7)
British Heart Foundation (RG/18/13/33946)
Wellcome Trust (204623/Z/16/Z)
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 (*). *The views expressed are those of the authors and not necessarily those of the NHS or the NIHR.