PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations.
Kamat, Mihir A
Staley, James R
Bioinformatics (Oxford, England)
Oxford University Press
MetadataShow full item record
Kamat, M. A., Blackshaw, J., Young, R., Surendran, P., Burgess, S., Danesh, J., Butterworth, A., & et al. (2019). PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations.. Bioinformatics (Oxford, England), 35 (22), 4851-4853. https://doi.org/10.1093/bioinformatics/btz469
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.
Humans, Genotype, Linkage Disequilibrium, Phenotype, Polymorphism, Single Nucleotide, Genome, Software, Genome-Wide Association Study, Genetic Association Studies
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 , 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.
European Research Council (268834)
British Heart Foundation (RG/13/13/30194)
Medical Research Council (MC_UU_00002/7)
British Heart Foundation (RG/18/13/33946)
External DOI: https://doi.org/10.1093/bioinformatics/btz469
This record's URL: https://www.repository.cam.ac.uk/handle/1810/293487
All rights reserved