{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:17Z","timestamp":1740185117619,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,12,13]],"date-time":"2019-12-13T00:00:00Z","timestamp":1576195200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"European Union\u2019s Horizon 2020","award":["GA 818110"],"award-info":[{"award-number":["GA 818110"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Over the past decade, there has been an exponential increase in the amount of disease-related genomic data available in public databases. However, this high-quality information is spread across independent sources and researchers often need to access these separately. Hence, there is a growing need for tools that gather and compile this information in an easy and automated manner. Here, we present \u2018VarGen\u2019, an easy-to-use, customizable R package that fetches, annotates and rank variants related to diseases and genetic disorders, using a collection public databases (viz. Online Mendelian Inheritance in Man, the Functional Annotation of the Mammalian genome 5, the Genotype-Tissue Expression and the Genome Wide Association Studies catalog). This package is also capable of annotating these variants to identify the most impactful ones. We expect that this tool will benefit the research of variant-disease relationships.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>VarGen is open-source and freely available via GitHub: https:\/\/github.com\/MCorentin\/VarGen. The software is implemented as an R package and is supported on Linux, MacOS and Windows.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz930","type":"journal-article","created":{"date-parts":[[2019,12,10]],"date-time":"2019-12-10T20:12:14Z","timestamp":1576008734000},"page":"2626-2627","source":"Crossref","is-referenced-by-count":0,"title":["VarGen: an R package for disease-associated variant discovery and annotation"],"prefix":"10.1093","volume":"36","author":[{"given":"Corentin","family":"Molitor","sequence":"first","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matt","family":"Brember","sequence":"additional","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7880-2519","authenticated-orcid":false,"given":"Fady","family":"Mohareb","sequence":"additional","affiliation":[{"name":"The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University , Bedford MK43 0AL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,12,13]]},"reference":[{"key":"2023013110255500400_btz930-B1","doi-asserted-by":"crossref","first-page":"1.2.1","DOI":"10.1002\/cpbi.27","article-title":"Searching Online Mendelian Inheritance in Man (OMIM): a knowledgebase of human genes and genetic phenotypes","volume":"58","author":"Amberger","year":"2017","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2023013110255500400_btz930-B2","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023013110255500400_btz930-B3","doi-asserted-by":"crossref","DOI":"10.4172\/jpb.1000455","article-title":"VarfromPDB: an automated and integrated tool to mine disease-gene-variant relations from the public databases and literature","author":"Cao","year":"2017","journal-title":"J. Proteomics Bioinformatics"},{"key":"2023013110255500400_btz930-B4","doi-asserted-by":"crossref","first-page":"121","DOI":"10.12688\/f1000research.13577.1","article-title":"Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies","volume":"7","author":"Ferrero","year":"2018","journal-title":"F1000Res"},{"key":"2023013110255500400_btz930-B5","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature24277","article-title":"Genetic effects on gene expression across human tissues","volume":"550","year":"2017","journal-title":"Nature"},{"key":"2023013110255500400_btz930-B6","doi-asserted-by":"crossref","first-page":"D833","DOI":"10.1093\/nar\/gkw943","article-title":"DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants","volume":"45","author":"Pinero","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023013110255500400_btz930-B7","doi-asserted-by":"crossref","first-page":"D886","DOI":"10.1093\/nar\/gky1016","article-title":"CADD: predicting the deleteriousness of variants throughout the human genome","volume":"47","author":"Rentzsch","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023013110255500400_btz930-B8","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":"2023013110255500400_btz930-B9","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1471-2164-10-22","article-title":"BioMart\u2014biological queries made easy","volume":"10","author":"Smedley","year":"2009","journal-title":"BMC Genomics"},{"key":"2023013110255500400_btz930-B10","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1038\/nbt.2422","article-title":"Interpreting noncoding genetic variation in complex traits and human disease","volume":"30","author":"Ward","year":"2012","journal-title":"Nat. Biotechnol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz930\/31720959\/btz930.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/8\/2626\/48984632\/bioinformatics_36_8_2626.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/8\/2626\/48984632\/bioinformatics_36_8_2626.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:26:01Z","timestamp":1675196761000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/8\/2626\/5675494"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,12,13]]},"references-count":10,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2020,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz930","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,4,15]]},"published":{"date-parts":[[2019,12,13]]}}}