Database of GENomic Variants of Oral Cancer: dbGENVOC

Nandini Pharasi, Jaypee Institute of Information Technology

Oral cancer, also known as mouth cancer develops in any part of the mouth due to genetic mutations. The reasons for this could be the usage of tobacco, heavy liquor, or human papillomavirus (HPV) infection. Symptoms include a lump or a red or white patch inside the mouth or a sore throat that doesn’t heal. Possible treatments could be surgery, radiation therapy and, chemotherapy in few cases. In Southeast Asia, especially in India, it is the most widespread form of cancer in men. Chewing tobacco has many side effects as unwanted mutations. Many research studies are going on to identify mutations that cause oral cancer.

Database of GENomic Variants of Oral Cancer:

India took part in ICGC (international cancer genome consortium) to generate large-scale genomic data on oral cancer patients and comprehensively cataloged associated variants. Department of biotechnology funded NIBGM (National Institute of Biomedical Genomics) is a self-governed institute in India. They altogether created a database of mutations in oral cancer. The world’s first-ever database on oral cancer mutations is named dbGENVOC (Database of GENomic Variants of Oral Cancer). dbGENVOC is a freely available database on the genomic variant of oral cancer that enables easy mining. It not only consists of genomic variants, but also it has a built-in powerful search engine. The repository is updated annually with the latest data of oral patients from different sections of the world.

Salient features of dbGENVOC:

1. Potential users can mine dbGENVOC on approximately 24 million pertinent germline and somatic variants from five whole-genome and hundred exome patients from India.
2. The database also incorporates some peer-reviewed publications and Cancer Genome Atlas of variant data.
3. Variants were annotated using multiple analytical and best practice protocols by the community.
4. Data for somatic variation were collected from 220 patients from the USA and was inspected by the TCGA (The Cancer Genome Atlas ) – HNSCC (head and neck cancer data) project.
5. The current database has very bounded information on oral cancer’s genomic variation.
6. dbGENVOC includes the TCGA-HNSCC project that doesn’t have any information on oral cancer genomic variants from India and Southeast Asia.
7. Similarly, it includes ICGS (International Cancer Genome Consortium) project database containing mutation primarily on somatic cells rather than oral cancer cells.
8. From a single portal, it allows cross-comparison of other datasets available.
9. Users need to register to access germline to avoid any ethical and data privacy issues.

This repository is going to support advance oral cancer researches by taking a major step from being just a catalog of variants to an insightful database. Users are allowed to search the database by multiple genes, multiple variant sites, a single gene genomic region, pathway identities, and patient ID. To conclude, we now know that dbGENVOC is a population-specific, large-scale, publically accessible database of oral cancer genomic variations. It might provide insightful knowledge to the researchers on a large scale as well as individual patient levels.

dbGENVOC Url: http://research.nibmg.ac.in/dbcares/dbgenvoc/

Also read: Do radiations from cell phone tend to cause cancer?

References:

• Sanchari Pradhan, Subrata Das, Animesh K Singh, Chitrarpita Das, Analabha Basu, Partha P Majumder, Nidhan K Biswas, dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India, Database, Volume 2021, 2021, baab034, https://academic.oup.com/database/article/doi/10.1093/database/baab034/6287646

• The Corrosion Prediction from the Corrosion Product Performance
• Nitrogen Resilience in Waterlogged Soybean plants
• Cell Senescence in Type II Diabetes: Therapeutic Potential
• Transgene-Free Canker-Resistant Citrus sinensis with Cas12/RNP
• AI Literacy in Early Childhood Education: Challenges and Opportunities