PhenoScanner: a database of human genotype–phenotype associations
By James R. Staley, James A. Blackshaw, M. Kamat, Steve Ellis, P. Surendran, Benjamin B. Sun, D. Paul, D. Freitag, Stephen Burgess, John Danesh and 2 more. Bioinform., 2016
1,277 citations recorded by the source corpus.
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.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/b92ed5d8103faf9ccdfd5d3c4f60b722866038d0
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In Genetics
- O. Yavors’ka
- Stephen Burgess
- Michael Inouye
- J. Bowden
- George Davey Smith
- Gibran Hemani
- S. Thompson
- E. Sanderson
In Molecular Biology
Citations in the corpus
- Allelic Landscape of Human Blood Cell Trait Variation and Links (2016, neutral): “…database (Landrum et al., 2016) https://www.ncbi.nlm.nih.gov/clinvar/ Variant Effect Predictor (McLaren et al., 2016) http://www.ensembl.org/info/docs/tools/vep/index.html PhenoScanner (Staley et al., 2016) http://www.phenoscanner.medschl.cam.ac.uk/phenoscanner”
- The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource (2022, background): “[5], ontology annotations [6] and curated top associations [7].”
- MendelianRandomization: an R package for performing Mendelian randomization analyses using summarized data (2017, methodology): “Finally, although the primary method for inputting data into the package is directly by the user, it is possible to incorporate data from PhenoScanner, a database of genotype—phenotype associations that can be queried using a web browser.(16) Two .”