Summary
Disease- and locus-specific variant databases have been a valuable resource to clinical and research geneticists. With the recent rapid developments in technologies, the number of DNA variants detected in a typical molecular genetics laboratory easily exceeds 1,000. To keep track of the growing inventory of DNA variants, many laboratories employ information technology to store the data as well as distributing the data and its associated information to clinicians and researchers via the Web. While it is a valuable resource, the hosting of a web-accessible database requires collaboration between bioinformaticians and biologists and careful planning to ensure its usability and availability. In this chapter, a series of tutorials on building a local DNA variant database out of a sample dataset will be provided. However, this tutorial will not include programming details on building a web interface and on constructing the web application necessary for web hosting. Instead, an introduction to the two commonly used methods for hosting web-accessible variant databases will be described. Apart from the tutorials, this chapter will also consider the resources and planning required for making a variant database project successful.
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Abbreviations
- cDNA:
-
copy or complementary DNA
- CGI:
-
common gateway interface
- CRC:
-
class responsibility collaboration
- DDL:
-
data definition language
- gDNA:
-
genomic DNA
- DBMS:
-
database management system
- HGVS:
-
Human Genome Variation Society
- HTML:
-
hypertext text markup language
- HUGO:
-
Human Genome Organization
- SQL:
-
structured query language
- OMIM:
-
Online Mendelian Inheritance in Man
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© 2008 Humana Press, a part of Springer Science+Business Media, LLC
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Fung, D.C. (2008). Developing a DNA Variant Database. In: Trent, R.J. (eds) Clinical Bioinformatics. Methods in Molecular Medicine™, vol 141. Humana Press. https://doi.org/10.1007/978-1-60327-148-6_12
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DOI: https://doi.org/10.1007/978-1-60327-148-6_12
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