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

Mihir Kamat; James Blackshaw; Robin Young; Praveen Surendran; Stephen Burgess; John Danesh; Adam S. Butterworth; James R Staley

doi:10.1093/bioinformatics/btz469

Abstract

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.

Keywords

PhenomePhenotypeBiologyLinkage disequilibriumComputational biologyGenetic associationGeneticsGenome-wide association studyPhenotypic traitEpigeneticsGenotypeGeneSingle-nucleotide polymorphism

MeSH Terms

Genetic Association StudiesGenomeGenome-Wide Association StudyGenotypeHumansLinkage DisequilibriumPhenotypePolymorphismSingle NucleotideSoftware

Affiliated Institutions

Related Publications

The allelic architecture of human disease genes: common disease-common variant... or not?

Jonathan K. Pritchard

Linkage disequilibrium (LD) plays a central role in current and proposed methods for mapping complex disease genes. LD-based methods work best when there is a single susceptibil...

2002 Human Molecular Genetics 712 citations

PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations

Joshua C. Denny , Marylyn D. Ritchie , Melissa Basford +7 more

Abstract Motivation: Emergence of genetic data coupled to longitudinal electronic medical records (EMRs) offers the possibility of phenome-wide association scans (PheWAS) for di...

2010 Bioinformatics 1285 citations

An Arabidopsis Example of Association Mapping in Structured Samples

Keyan Zhao , María José Aranzana , Sung Hoon Kim +8 more

A potentially serious disadvantage of association mapping is the fact that marker-trait associations may arise from confounding population structure as well as from linkage to c...

2007 PLoS Genetics 724 citations

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

Chi Zhang , Shan‐Shan Dong , Junyang Xu +2 more

Abstract Motivation Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay analysis from variant ...

2018 Bioinformatics 1815 citations

Fine mapping of the association with obesity at the FTO locus in African-derived populations

Mohamed Hassanein , Helen N. Lyon , Thutrang Nguyen +19 more

Genome-wide association studies have identified many common genetic variants that are associated with polygenic traits, and have typically been performed with individuals of rec...

2010 Human Molecular Genetics 90 citations

Publication Info

Year: 2019
Type: article
Volume: 35
Issue: 22
Pages: 4851-4853
Citations: 2334
Access: Closed

External Links

Download PDF (Free) View on DOI.org PubMed Semantic Scholar

Social Impact

Altmetric

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

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

2334

OpenAlex

Influential

1787

CrossRef

Cite This

APA Style

                            
                                
                                    Mihir Kamat, 
                                
                                    James Blackshaw, 
                                
                                    Robin Young
                                
                                et al.
                            
                            (2019). 
                            PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations. 
                            Bioinformatics
                            , 35
                            (22)
                            , 4851-4853.
                            https://doi.org/10.1093/bioinformatics/btz469
                        

Identifiers

DOI: 10.1093/bioinformatics/btz469
PMID: 31233103
PMCID: PMC6853652

Data Quality

Data completeness: 90%