What is a gene/disease specific database?
Gene/disease specific databases (G/DSDBs), gene variant or locus specific databases (LSDBs) are used to collate and provide information on gene and protein variations that have relevance to disease .
The primary purpose of a gene/disease specific database is to provide access for clinicians, scientists, and the wider community to information on known genetic variants and clinically relevant data on a gene by gene basis .
Published and unpublished (direct laboratory submitted) data on variation relating to a specific gene are deposited into these databases. Some databases contain extensive amounts of information, and are excellent resources and knowledge bases .
Ideal gene/disease specific databases:
- Contain gene specific information with all known variations .
- Are regularly maintained and contain current up to date data .
- Are curated by experts in the field; involving collaboration by a consortium of scientific researches with expertise in the particular gene(s) .
- Provide excellent reliable data with clinical grade interpretation on variants in collaboration with an expert clinical Interpretation committee .
The information recorded in individual databases will vary dependent on the gene of interest, whether associated diseases are common or rare, and whether phenotypic information is available.
Examples of Gene/Disease Specific Databases
The Human Variome Project maintains a list of known gene/disease specific databases.
Notable examples include:
- The International Society for Gastrointestinal Hereditary Tumors Colon cancer gene variant databases
- 1.Vihinen, M., Dunnen, J.T. den, Dalgleish, R., and Cotton, R.G.H. Guidelines for establishing locus specific databases. Human Mutation 33, 2 (2012), 298–305.
- 2.Celli, J., Dalgleish, R., Vihinen, M., Taschner, P.E.M., and Dunnen J.T., den. Curating gene variant databases (LSDBs): Toward a universal standard. Human Mutation 33, 2 (2012), 291–297.
- 3.Mitropoulou, C., Webb, A.J., Mitropoulos, K., Brookes, A.J., and Patrinos, G.P. Locus-specific database domain and data content analysis: evolution and content maturation toward clinical use. Human Mutation 31, 10 (2010), 1109–1116.
- 4.Thompson, B.A., Spurdle, A.B., Plazzer, J.-P., et al. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nature Genetics 46, 2 (2014), 107–115.