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

Research output: Contribution to journalArticle

  • Mihir A Kamat
  • James A Blackshaw
  • Robin Young
  • Praveen Surendran
  • Stephen Burgess
  • John Danesh
  • Adam S Butterworth
  • James R Staley
Original languageEnglish
Article numberbtz469
Number of pages3
JournalBioinformatics
DOIs
DateAccepted/In press - 19 Jun 2019
DatePublished (current) - 24 Jun 2019

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.

SUPPLEMENTARY INFORMATION: Full documentation: www.phenoscanner.medschl.cam.ac.uk/information.

Additional information

© The Author(s) 2019. Published by Oxford University Press.

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    Rights statement: This is the final published version of the article (version of record). It first appeared online via Oxford University Press at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz469/5522366. Please refer to any applicable terms of use of the publisher.

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