The National Institute of Biomedical Genomics (NIBMG), a research institute for genomic medicine in India, has created a database of genomic variations in oral cancer; the first of its kind in the world.
The institute, located at Kalyani, 50 km from Kolkata, under the Department of Biotechnology, has made this database publicly-accessible, official sources said on Wednesday.
dbGENVOC is a browsable online database of GENomic Variants of Oral Cancer and is a free resource. 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.
dbGENVOC is not just a catalogue of genomic variants, it has a built-in powerful search engine. It also allows a reasonable extent of statistical and bioinformatic analysis to be carried out online, including identifying variants in associated altered pathways in oral cancer.
The repository, which will be updated annually with variation data from new oral cancer patients from different regions of India and southeast Asia, has the potential to support advances in oral cancer research and will be a major step in moving forward from simply cataloguing variants to gain insight into their significance.
Oral cancer is the most prevalent form of cancer among men in India, largely fuelled by tobacco-chewing. Tobacco-chewing causes changes in the genetic material of cells in the oral cavity. These changes (mutations) precipitate oral cancer. Research to identify those genetic mutations that drive oral cancer are ongoing. Such driver mutations may be variable across populations.
The URL for the database, dbGENVOC, is: DATABASE http://research.nibmg.ac.in/dbcares/dbgenvoc/