{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,6]],"date-time":"2024-09-06T11:01:13Z","timestamp":1725620473475},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Dravet Foundation Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"Abstract<\/jats:title>\n Clinical genetic testing has exponentially expanded in recent years, leading to an overwhelming amount of patient variants with high variability in pathogenicity and heterogeneous phenotypes. A large part of the variant level data is aggregated in public databases such as ClinVar. However, the ability to explore this rich resource and answer general questions such as \u2018How many genes inside ClinVar are associated with a specific disease? or \u2018In which part of the protein are patient variants located?\u2019 is limited and requires advanced bioinformatics processing. Here, we present Simple ClinVar (http:\/\/simple-clinvar.broadinstitute.org\/) a web server application that is able to provide variant, gene and disease level summary statistics based on the entire ClinVar database in a dynamic and user-friendly web-interface. Overall, our web application is able to interactively answer basic questions regarding genetic variation and its known relationships to disease. By typing a disease term of interest, the user can identify in seconds the genes and phenotypes most frequently reported to ClinVar. Subsets of variants can then be further explored, filtered or mapped and visualized in the corresponding protein sequences. Our website will follow ClinVar monthly releases and provide easy access to ClinVar resources to a broader audience including basic and clinical scientists.<\/jats:p>","DOI":"10.1093\/nar\/gkz411","type":"journal-article","created":{"date-parts":[[2019,5,20]],"date-time":"2019-05-20T19:18:23Z","timestamp":1558379903000},"page":"W99-W105","source":"Crossref","is-referenced-by-count":51,"title":["Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database"],"prefix":"10.1093","volume":"47","author":[{"ORCID":"http:\/\/orcid.org\/0000-0003-0546-5141","authenticated-orcid":false,"given":"Eduardo","family":"P\u00e9rez-Palma","sequence":"first","affiliation":[{"name":"Cologne Center for Genomics, University of Cologne, 50939\u00a0Cologne, NRW, Germany"}]},{"given":"Marie","family":"Gramm","sequence":"additional","affiliation":[{"name":"Cologne Center for Genomics, University of Cologne, 50939\u00a0Cologne, NRW, Germany"}]},{"given":"Peter","family":"N\u00fcrnberg","sequence":"additional","affiliation":[{"name":"Cologne Center for Genomics, University of Cologne, 50939\u00a0Cologne, NRW, Germany"}]},{"ORCID":"http:\/\/orcid.org\/0000-0001-8698-3770","authenticated-orcid":false,"given":"Patrick","family":"May","sequence":"additional","affiliation":[{"name":"Luxembourg Centre for Systems Biomedicine, University Luxembourg, L-4362\u00a0Esch-sur-Alzette, Luxembourg"}]},{"given":"Dennis","family":"Lal","sequence":"additional","affiliation":[{"name":"Cologne Center for Genomics, University of Cologne, 50939\u00a0Cologne, NRW, Germany"},{"name":"Epilepsy Center, Neurological Institute, Cleveland Clinic, 44195\u00a0Cleveland, OH,\u00a0USA"},{"name":"Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic,\u00a044195\u00a0Cleveland, OH, USA"},{"name":"Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 02142 Cambridge, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2020071700303868300_B1","doi-asserted-by":"crossref","first-page":"D1062","DOI":"10.1093\/nar\/gkx1153","article-title":"ClinVar: improving access to variant interpretations and supporting evidence","volume":"46","author":"Landrum","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020071700303868300_B2","first-page":"8.16.11","article-title":"Using ClinVar as a resource to support variant interpretation","volume":"89","author":"Harrison","year":"2016","journal-title":"Curr. Protoc. Hum. Genet."},{"key":"2020071700303868300_B3","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2020071700303868300_B4","doi-asserted-by":"crossref","first-page":"D7","DOI":"10.1093\/nar\/gkv1290","article-title":"Database resources of the National Center for Biotechnology Information","volume":"44","author":"Coordinators, N.R.","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020071700303868300_B5","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O\u2019Leary","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020071700303868300_B6","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1002\/humu.22981","article-title":"HGVS recommendations for the description of sequence variants: 2016 Update","volume":"37","author":"den\u00a0Dunnen","year":"2016","journal-title":"Hum. Mutat."},{"key":"2020071700303868300_B7","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1002\/humu.23555","article-title":"ClinVar Miner: Demonstrating utility of a Web-based tool for viewing and filtering ClinVar data","volume":"39","author":"Henrie","year":"2018","journal-title":"Hum. Mutat."},{"key":"2020071700303868300_B8","doi-asserted-by":"crossref","first-page":"33","DOI":"10.12688\/wellcomeopenres.11640.1","article-title":"ClinVar data parsing","volume":"2","author":"Zhang","year":"2017","journal-title":"Wellcome Open Res."},{"key":"2020071700303868300_B9","doi-asserted-by":"crossref","first-page":"462","DOI":"10.12688\/f1000research.14470.2","article-title":"Clinotator: analyzing ClinVar variation reports to prioritize reclassification efforts [version 2; peer review: 2 approved]","volume":"7","author":"Butler\u00a0Iii","year":"2018","journal-title":"F1000Res"},{"key":"2020071700303868300_B10","doi-asserted-by":"crossref","first-page":"D862","DOI":"10.1093\/nar\/gkv1222","article-title":"ClinVar: public archive of interpretations of clinically relevant variants","volume":"44","author":"Landrum","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020071700303868300_B11","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"2020071700303868300_B12","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The UniProt, C.","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020071700303868300_B13","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med."},{"key":"2020071700303868300_B14","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60,706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"2020071700303868300_B15","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1002\/humu.10212","article-title":"Human Gene Mutation Database (HGMD): 2003 update","volume":"21","author":"Stenson","year":"2003","journal-title":"Hum. Mutat."},{"key":"2020071700303868300_B16","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1002\/humu.21438","article-title":"LOVD v.2.0: the next generation in gene variant databases","volume":"32","author":"Fokkema","year":"2011","journal-title":"Hum. Mutat."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/W1\/W99\/28880104\/gkz411.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/W1\/W99\/28880104\/gkz411.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,17]],"date-time":"2020-07-17T14:19:38Z","timestamp":1594995578000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/W1\/W99\/5494761"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,22]]},"references-count":16,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2019,5,22]]},"published-print":{"date-parts":[[2019,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz411","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.735809666.793560998","asserted-by":"object"}]},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,7,2]]},"published":{"date-parts":[[2019,5,22]]}}}
