dbGENVOC, a comprehensive, flexible database framework, developed with an aim to allow potential users to access, query, browse and download clinically relevant somatic and germline variation data from Indian oral cancer patients. This database will store variant calls from various studies that uses massively parallel sequencing to generate genome-scale data. First release of dbGENVOC contains (i) ~24 million somatic and germline variants derived from whole exome sequences of 100 Indian oral cancer patients and whole genome sequences of 5 oral cancer patients from India, (ii) somatic variation data from 220 patient samples drawn from the USA and analyzed by TCGA-HNSCC project and (iii) manually curated variation data of 118 patients from recently published peer-reviewed publications. Variants were identified by the community approved best practice protocol and annotated using multiple analytic pipeline. This repository has the potential to support advances in oral cancer research and will be a major step in moving forward from simply cataloging variants to gain insight into their significance. It is freely available and will be updated frequently with variation data from additional oral cancer patients.
Table 1. Summary of germline and somatic variants integrated in dbGENVOC
The home page introduces a live search box. User can go to the 'Result' page directly by entering gene name, genomic region, multiple gene names,multi-sites in the ‘Home’ page search box. Gene name auto spell checking (It will check if user has entered a proper human gene name or not) option are active in home page search box. At the top right corner comprised of three different link buttons “Home”, “Help” and “Contact Us”. Clicking on these buttons user can go to the respective pages.
(a) Gene: Since there are alternative names for the genes, a search can be performed by any gene symbol or alias or gene name of a particular gene (e.g BRCA2).
(b) Genomic region: On the basis of genomic region (e.g. 1:915188-1015188) a search can be performed to get specific details of the mutation spectrum on a particular chromosomal region. For timely return of results, query region size are limited to 100KB.
(c) multi-gene (e.g. TP53 BRCA2 NOTCH1)
(d) multi-sites (e.g. chr11:534289,chr17:7578406,chr17:7577538,chr17:7577120)
(e) patient id (e.g. NIBMG-F316-GB, TCGA-BA-7269-01A-11D, OT54)
(f) Pathway based search (e.g. Wnt signaling pathway)
From this page users can get detail variant information about the respective gene/region in which they are interested. To view exome, whole genome somatic or germline data user has to click the ‘Somatic’ or ‘Germline’ button under ‘Exome’, ‘Whole genome’ respectively. The result page contains three panels; top panel represents a table enlisting all the detail variants information from dbgenvoc for respective searched gene/region. Middle panel represents a table enlisting all the detail variants information from TCGA Oral cancer data for respective searched gene/region. Bottom panel represents variations from peer-reviewed papers.
View: Rows number of search result can be changed from drop down list.
Search within search result: Entering search term in search box present above data table in ‘result page’.
Sorting: Sort data clicking on column name.
Show / Hide Column: Disabling features (columns) that user does not wish to use.
Download option: Search result can be downloaded in excel format.