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

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

doi:10.1093/bioinformatics/btz469

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

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

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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.

Original language	English
Article number	btz469
Number of pages	3
Journal	Bioinformatics
DOIs	https://doi.org/10.1093/bioinformatics/btz469
Publication status	Published - 24 Jun 2019

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@article{32a35aec937440f4972766d136f6234a,

title = "PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations",

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.",

author = "Kamat, {Mihir A} and Blackshaw, {James A} and Robin Young and Praveen Surendran and Stephen Burgess and John Danesh and Butterworth, {Adam S} and Staley, {James R}",

note = "{\textcopyright} The Author(s) 2019. Published by Oxford University Press.",

year = "2019",

month = jun,

day = "24",

doi = "10.1093/bioinformatics/btz469",

language = "English",

journal = "Bioinformatics",

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TY - JOUR

T1 - PhenoScanner V2

T2 - an expanded tool for searching human genotype-phenotype associations

AU - Kamat, Mihir A

AU - Blackshaw, James A

AU - Young, Robin

AU - Surendran, Praveen

AU - Burgess, Stephen

AU - Danesh, John

AU - Butterworth, Adam S

AU - Staley, James R

PY - 2019/6/24

Y1 - 2019/6/24

N2 - 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.

AB - 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.

U2 - 10.1093/bioinformatics/btz469

DO - 10.1093/bioinformatics/btz469

M3 - Article (Academic Journal)

C2 - 31233103

SN - 1367-4803

JO - Bioinformatics

JF - Bioinformatics

M1 - btz469

ER -

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

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