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...
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| Veröffentlicht in: | Bioinformatics 2019-11, Vol.35 (22), p.4851-4853 |
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| container_title | Bioinformatics |
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| creator | Kamat, Mihir A Blackshaw, James A Young, Robin Surendran, Praveen Burgess, Stephen Danesh, John Butterworth, Adam S Staley, James R |
| description | 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. |
| doi_str_mv | 10.1093/bioinformatics/btz469 |
| format | Article |
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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.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btz469</identifier><identifier>PMID: 31233103</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Applications Notes ; Genetic Association Studies ; Genome ; Genome-Wide Association Study ; Genotype ; Humans ; Linkage Disequilibrium ; Phenotype ; Polymorphism, Single Nucleotide ; Software</subject><ispartof>Bioinformatics, 2019-11, Vol.35 (22), p.4851-4853</ispartof><rights>The Author(s) 2019. Published by Oxford University Press. 2019</rights><rights>The Author(s) 2019. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c518t-20215a4f617f52135b743479b785cc74a06534b7c9de93c52cba0a28eed348f13</citedby><cites>FETCH-LOGICAL-c518t-20215a4f617f52135b743479b785cc74a06534b7c9de93c52cba0a28eed348f13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853652/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853652/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,882,1599,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31233103$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Kelso, Janet</contributor><creatorcontrib>Kamat, Mihir A</creatorcontrib><creatorcontrib>Blackshaw, James A</creatorcontrib><creatorcontrib>Young, Robin</creatorcontrib><creatorcontrib>Surendran, Praveen</creatorcontrib><creatorcontrib>Burgess, Stephen</creatorcontrib><creatorcontrib>Danesh, John</creatorcontrib><creatorcontrib>Butterworth, Adam S</creatorcontrib><creatorcontrib>Staley, James R</creatorcontrib><title>PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>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.</description><subject>Applications Notes</subject><subject>Genetic Association Studies</subject><subject>Genome</subject><subject>Genome-Wide Association Study</subject><subject>Genotype</subject><subject>Humans</subject><subject>Linkage Disequilibrium</subject><subject>Phenotype</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Software</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqNUctKxDAUDaI44-MTlC7djObd1oUg4gsEBV_LkKbpNNImNWlFXfkP_qFfYmTGwdm5ugfuecEBYAfBfQRzclAYZ2zlfCt7o8JB0b9Tnq-AMaIcTjBk-WrEhKcTmkEyAhshPEHIEKV0HYwIwoQgSMbg8abW1t0qaa32yQM-TKRN9GsnbanLpHeuSWJIErT0qjZ2mtRDGxnTKOrfOv318dnVc5zIEJwysY-zYQusVbIJent-N8H92endycXk6vr88uT4aqIYyvpYFCMmacVRWjGMCCtSSmiaF2nGlEqphJwRWqQqL3VOFMOqkFDiTOuS0KxCZBMczXy7oWh1qbTtvWxE500r_Ztw0ojljzW1mLoXwTNGOMPRYG9u4N3zoEMvWhOUbhpptRuCwJhyTDPGf7LYjKq8C8HrahGDoPgZRSyPImajRN3u344L1e8KkQBnBDd0__T8BhiRolk</recordid><startdate>20191101</startdate><enddate>20191101</enddate><creator>Kamat, Mihir A</creator><creator>Blackshaw, James A</creator><creator>Young, Robin</creator><creator>Surendran, Praveen</creator><creator>Burgess, Stephen</creator><creator>Danesh, John</creator><creator>Butterworth, Adam S</creator><creator>Staley, James R</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20191101</creationdate><title>PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations</title><author>Kamat, Mihir A ; Blackshaw, James A ; Young, Robin ; Surendran, Praveen ; Burgess, Stephen ; Danesh, John ; Butterworth, Adam S ; Staley, James R</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c518t-20215a4f617f52135b743479b785cc74a06534b7c9de93c52cba0a28eed348f13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Applications Notes</topic><topic>Genetic Association Studies</topic><topic>Genome</topic><topic>Genome-Wide Association Study</topic><topic>Genotype</topic><topic>Humans</topic><topic>Linkage Disequilibrium</topic><topic>Phenotype</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kamat, Mihir A</creatorcontrib><creatorcontrib>Blackshaw, James A</creatorcontrib><creatorcontrib>Young, Robin</creatorcontrib><creatorcontrib>Surendran, Praveen</creatorcontrib><creatorcontrib>Burgess, Stephen</creatorcontrib><creatorcontrib>Danesh, John</creatorcontrib><creatorcontrib>Butterworth, Adam S</creatorcontrib><creatorcontrib>Staley, James R</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kamat, Mihir A</au><au>Blackshaw, James A</au><au>Young, Robin</au><au>Surendran, Praveen</au><au>Burgess, Stephen</au><au>Danesh, John</au><au>Butterworth, Adam S</au><au>Staley, James R</au><au>Kelso, Janet</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2019-11-01</date><risdate>2019</risdate><volume>35</volume><issue>22</issue><spage>4851</spage><epage>4853</epage><pages>4851-4853</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>31233103</pmid><doi>10.1093/bioinformatics/btz469</doi><tpages>3</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford Journals Open Access Collection; PubMed Central; Alma/SFX Local Collection |
| subjects | Applications Notes Genetic Association Studies Genome Genome-Wide Association Study Genotype Humans Linkage Disequilibrium Phenotype Polymorphism, Single Nucleotide Software |
| title | PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations |
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