DriverDB: an exome sequencing database for cancer driver gene identification

Developers

Wei-Chung Cheng, I-Fang Chung, Chen-Yang Chen, etc.

Description of the technology

Exome sequencing (exome-seq) has aided in the discovery of a huge amount of mutations in cancers, yet challenges remain in converting oncogenomics data into information that is interpretable and accessible for clinical care. It remains a significant challenge to identify cancer driver mutations and driver genes.
Taiwanese scientists constructed DriverDB (http://ngs.ym.edu.tw/driverdb/), a database which incorporates 6079 cases of exome-seq data, annotation databases (such as dbSNP, 1000 Genome and Cosmic) and published bioinformatics algorithms dedicated to driver gene/mutation identification. DriverDB focuses on predicting driver genes by various algorithms and provides different aspects of the mutation profiles of an individual gene.

DriverDB provides two points of view, ‘Cancer’ and ‘Gene’, to help researchers to visualize the relationships between cancers and driver genes/mutations. The ‘Cancer’ section summarizes the calculated results of driver genes by eight computational methods for a specific cancer type/dataset and provides three levels of biological interpretation for realization of the relationships between driver genes. The ‘Gene’ section is designed to visualize the mutation information of a driver gene in five different aspects. Moreover, a ‘Meta-Analysis’ function is provided so researchers may identify driver genes in customer-defined samples.

Practical application

The novel driver genes/mutations identified using DriverDB hold potential for both basic research and biotech applications.

Laboratories

• Pediatric Neurosurgery, Department of Surgery, Cheng Hsin General Hospital, Taipei, (Taiwan)
• VGH-YM Genomic Research Center, National Yang-Ming University, Taipei, (Taiwan)
• Institute of Biomedical Informatics, National Yang-Ming University, Taipei, (Taiwan)
• Information Technology Office, Taipei Veterans General Hospital, Taipei, (Taiwan)
• Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, (Taiwan)
• Department of Education and Research, Taipei City Hospital, Taipei, (Taiwan)

Links

http://nar.oxfordjournals.org/content/42/D1/D1048.full.pdf+html

Publications

• Cheng, Wei-Chung, et al. "DriverDB: an exome sequencing database for cancer driver gene identification." Nucleic acids research 42.D1 (2014): D1048-D1054.
• Gnad, Florian, et al. "Assessment of computational methods for predicting the effects of missense mutations in human cancers." BMC genomics 14.3 (2013): 1.
• Carter, Hannah, et al. "Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations." Cancer research 69.16 (2009): 6660-6667.
• Zhao, Huiying, et al. "DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels." Genome biology 14.3 (2013): 1.
• Li, Miao-Xin, et al. "Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies." PLoS Genet 9.1 (2013): e1003143.