{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T10:37:28Z","timestamp":1772015848106,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,5,28]],"date-time":"2021-05-28T00:00:00Z","timestamp":1622160000000},"content-version":"vor","delay-in-days":27,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["BT\/PR16536\/BID\/7\/652\/2016"],"award-info":[{"award-number":["BT\/PR16536\/BID\/7\/652\/2016"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["SyMeC:BT\/MED-II\/NIBMG\/SyMeC\/2014\/Vol-II"],"award-info":[{"award-number":["SyMeC:BT\/MED-II\/NIBMG\/SyMeC\/2014\/Vol-II"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Oral cancer is highly prevalent in India and is the most frequent cancer type among Indian males. It is also very common in southeast Asia. India has participated in the International Cancer Genome Consortium (ICGC) and some national initiatives to generate large-scale genomic data on oral cancer patients and analyze to identify associations and systematically catalog the associated variants. We have now created an open, web-accessible database of these variants found significantly associated with Indian oral cancer patients, with a user-friendly interface to enable easy mining. We have value added to this database by including relevant data collated from various sources on other global populations, thereby providing opportunities of comparative geographical and\/or ethnic analyses. Currently, no other database of similar nature is available on oral cancer. We have developed Database of GENomic Variants of Oral Cancer, a browsable online database framework for storage, retrieval and analysis of large-scale data on genomic variants and make it freely accessible to the scientific community. Presently, the web-accessible database allows potential users to mine data on \u223c24\u2009million clinically relevant somatic and germline variants derived from exomes (n\u2009=\u2009100) and whole genomes (n\u2009=\u20095) of Indian oral cancer patients; all generated by us. Variant data from The Cancer Genome Atlas and data manually curated from peer-reviewed publications were also incorporated into the database for comparative analyses. It allows users to query the database by a single gene, multiple genes, multiple variant sites, genomic region, patient ID and pathway identities.<\/jats:p>\n               <jats:p>Database URL: http:\/\/research.nibmg.ac.in\/dbcares\/dbgenvoc\/<\/jats:p>","DOI":"10.1093\/database\/baab034","type":"journal-article","created":{"date-parts":[[2021,5,16]],"date-time":"2021-05-16T03:07:46Z","timestamp":1621134466000},"source":"Crossref","is-referenced-by-count":12,"title":["dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India"],"prefix":"10.1093","volume":"2021","author":[{"given":"Sanchari","family":"Pradhan","sequence":"first","affiliation":[{"name":"Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India"}]},{"given":"Subrata","family":"Das","sequence":"additional","affiliation":[{"name":"Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India"}]},{"given":"Animesh K","family":"Singh","sequence":"additional","affiliation":[{"name":"Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India"}]},{"given":"Chitrarpita","family":"Das","sequence":"additional","affiliation":[{"name":"Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India"}]},{"given":"Analabha","family":"Basu","sequence":"additional","affiliation":[{"name":"Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India"}]},{"given":"Partha P","family":"Majumder","sequence":"additional","affiliation":[{"name":"Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India"},{"name":"Human Genetics Unit, Indian Statistical Institute, Kolkata, West Bengal 700108, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7960-3290","authenticated-orcid":false,"given":"Nidhan K","family":"Biswas","sequence":"additional","affiliation":[{"name":"Human Genetics Unit, National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India"}]}],"member":"286","published-online":{"date-parts":[[2021,5,28]]},"reference":[{"key":"2021070818443107200_R1","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1016\/j.semcancer.2018.01.008","article-title":"Head and neck squamous cell carcinoma: genomics and emerging biomarkers for immunomodulatory cancer treatments","volume":"52","author":"Solomon","year":"2018","journal-title":"Semin. Cancer Biol."},{"key":"2021070818443107200_R2","doi-asserted-by":"crossref","DOI":"10.1038\/sj.bdj.2017.293","article-title":"Oral cancer: Indian pandemic","volume":"222","author":"Gupta","year":"2017","journal-title":"Br. Dent. J."},{"key":"2021070818443107200_R3","doi-asserted-by":"crossref","first-page":"A68","DOI":"10.5114\/wo.2014.47136","article-title":"The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge","volume":"19","author":"Tomczak","year":"2015","journal-title":"Wspolczesna Onkol"},{"key":"2021070818443107200_R4","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nature08987","article-title":"International network of cancer genome projects","volume":"464","author":"Hudson","year":"2010","journal-title":"Nature"},{"key":"2021070818443107200_R5","first-page":"1","article-title":"APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism","volume":"8","author":"Chen","year":"2017","journal-title":"Nat. Commun."},{"key":"2021070818443107200_R6","first-page":"1","article-title":"Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups","volume":"4","author":"Maitra","year":"2013","journal-title":"Nat. Commun."},{"key":"2021070818443107200_R7","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.oraloncology.2017.08.003","article-title":"Genomic characterization of tobacco\/nut chewing HPV-negative early stage tongue tumors identify MMP10 as a candidate to predict metastases","volume":"73","author":"Upadhyay","year":"2017","journal-title":"Oral Oncol."},{"key":"2021070818443107200_R8","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.gpb.2018.03.005","article-title":"CCGD-ESCC: a comprehensive database for genetic variants associated with esophageal squamous cell carcinoma in Chinese population","volume":"16","author":"Peng","year":"2018","journal-title":"Genomics Proteomics Bioinform"},{"key":"2021070818443107200_R9","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1002\/humu.20495","article-title":"Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database","volume":"28","author":"Petitjean","year":"2007","journal-title":"Hum. Mutat."},{"key":"2021070818443107200_R10","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1093\/nar\/26.1.205","article-title":"IARC database of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation tools","volume":"26","author":"Hainaut","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"2021070818443107200_R11","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nrc1299","article-title":"A census of human cancer genes","volume":"4","author":"Futreal","year":"2004","journal-title":"Nat. Rev. Cancer"},{"key":"2021070818443107200_R12","doi-asserted-by":"crossref","first-page":"D945","DOI":"10.1093\/nar\/gkq929","article-title":"COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer","volume":"39","author":"Forbes","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2021070818443107200_R13","doi-asserted-by":"crossref","first-page":"D836","DOI":"10.1093\/nar\/gkm730","article-title":"MethyCancer: the database of human DNA methylation and cancer","volume":"36","author":"He","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2021070818443107200_R14","doi-asserted-by":"crossref","first-page":"D658","DOI":"10.1093\/nar\/gkp933","article-title":"dbDEPC: a database of differentially expressed proteins in human cancers","volume":"38","author":"Li","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2021070818443107200_R15","doi-asserted-by":"crossref","first-page":"D964","DOI":"10.1093\/nar\/gkr936","article-title":"dbDEPC 2.0: updated database of differentially expressed proteins in human cancers","volume":"40","author":"He","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2021070818443107200_R16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/database\/bay015","article-title":"DbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication","volume":"2018","author":"Yang","year":"2018","journal-title":"Database"},{"key":"2021070818443107200_R17","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.oraloncology.2011.09.014","article-title":"HNOCDB: a comprehensive database of genes and miRNAs relevant to head and neck and oral cancer","volume":"48","author":"Mitra","year":"2012","journal-title":"Oral Oncol."},{"key":"2021070818443107200_R18","doi-asserted-by":"crossref","DOI":"10.1016\/j.oraloncology.2012.02.006","article-title":"OrCa-dB: a complete catalogue of molecular and clinical information in oral carcinogenesis","volume":"48","author":"Reshmi","year":"2012","journal-title":"Oral Oncol."},{"key":"2021070818443107200_R19","first-page":"41","article-title":"Database and interactome map of genes involved in oral cancer","volume":"8","author":"Gadewal","year":"2007","journal-title":"Online J. Bioinform."},{"key":"2021070818443107200_R20","doi-asserted-by":"crossref","first-page":"169","DOI":"10.6026\/97320630006169","article-title":"Database and interaction network of genes involved in oral cancer: version II","volume":"6","author":"Gadewal","year":"2011","journal-title":"Bioinformation"},{"key":"2021070818443107200_R21","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1093\/nar\/29.1.300","article-title":"OrCGDB: a database of genes involved in oral cancer","volume":"29","author":"Levine","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2021070818443107200_R22","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.2004088","article-title":"Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal","volume":"6","author":"Gao","year":"2013","journal-title":"Sci. Signal."},{"key":"2021070818443107200_R23","article-title":"Integrated analysis of oral tongue squamous cell carcinoma identifies key variants and pathways linked to risk habits, HPV, clinical parameters and tumor recurrence","volume":"4","author":"Panda","year":"2015","journal-title":"F1000Research"},{"key":"2021070818443107200_R24","article-title":"[Heng Li - compares BWA to other long read aligners like CUSHAW2] Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","volume-title":"arXiv Prepr. arXiv","author":"Li","year":"2013"},{"key":"2021070818443107200_R25","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"Depristo","year":"2011","journal-title":"Nat. Genet."},{"key":"2021070818443107200_R26","first-page":"262","article-title":"MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data","volume":"16","author":"Fan","year":"2016","journal-title":"Genome Biol."},{"key":"2021070818443107200_R27","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"Cibulskis","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"2021070818443107200_R28","doi-asserted-by":"crossref","DOI":"10.1101\/861054","article-title":"Calling Somatic SNVs and Indels with Mutect2","author":"Benjamin","year":"2019"},{"key":"2021070818443107200_R29","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/s41592-018-0051-x","article-title":"Strelka2: fast and accurate calling of germline and somatic variants","volume":"15","author":"Kim","year":"2018","journal-title":"Nat. Methods"},{"key":"2021070818443107200_R30","doi-asserted-by":"crossref","DOI":"10.1101\/201178","article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples","volume-title":"bioRxiv","author":"Poplin","year":"2017"},{"key":"2021070818443107200_R31","doi-asserted-by":"crossref","first-page":"E2423","DOI":"10.1002\/humu.22771","article-title":"Oncotator: cancer variant annotation tool","volume":"36","author":"Ramos","year":"2015","journal-title":"Hum. Mutat."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baab034\/38373939\/baab034.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baab034\/38373939\/baab034.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,9]],"date-time":"2021-07-09T02:17:54Z","timestamp":1625797074000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baab034\/6287646"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,1]]},"references-count":31,"URL":"https:\/\/doi.org\/10.1093\/database\/baab034","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,5,1]]},"published":{"date-parts":[[2021,5,1]]},"article-number":"baab034"}}