PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 11 2019
01 11 2019
Historique:
received:
20
12
2018
revised:
01
05
2019
accepted:
19
06
2019
pubmed:
25
6
2019
medline:
25
6
2020
entrez:
25
6
2019
Statut:
ppublish
Résumé
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. PhenoScanner V2 is available at www.phenoscanner.medschl.cam.ac.uk.
Identifiants
pubmed: 31233103
pii: 5522366
doi: 10.1093/bioinformatics/btz469
pmc: PMC6853652
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4851-4853Subventions
Organisme : Medical Research Council
ID : MR/L003120/1
Pays : United Kingdom
Organisme : British Heart Foundation
ID : RG/13/13/30194
Pays : United Kingdom
Organisme : Medical Research Council
ID : G0800270
Pays : United Kingdom
Organisme : Department of Health
Pays : United Kingdom
Organisme : British Heart Foundation
ID : SP/09/002
Pays : United Kingdom
Organisme : European Research Council
ID : 268834
Pays : International
Organisme : Medical Research Council
ID : MR/S003746/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_00002/7
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 204623/Z/16/Z
Pays : United Kingdom
Organisme : British Heart Foundation
ID : RG/18/13/33946
Pays : United Kingdom
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
Références
Nature. 2018 Jun;558(7708):73-79
pubmed: 29875488
Bioinformatics. 2012 Jul 15;28(14):1919-20
pubmed: 22576172
Nucleic Acids Res. 2001 Jan 1;29(1):308-11
pubmed: 11125122
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Cell. 2016 Nov 17;167(5):1415-1429.e19
pubmed: 27863252
Nature. 2017 Oct 11;550(7675):204-213
pubmed: 29022597
Bioinformatics. 2016 Oct 15;32(20):3207-3209
pubmed: 27318201
Genome Res. 2012 Sep;22(9):1760-74
pubmed: 22955987
Circ Res. 2018 Feb 2;122(3):433-443
pubmed: 29212778
Nucleic Acids Res. 2017 Jan 4;45(D1):D896-D901
pubmed: 27899670
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Bioinformatics. 2010 Apr 15;26(8):1112-8
pubmed: 20200009