eMelanoBase: An online locus-specific variant database for familial melanoma

Fung, David C.Y., Holland, Elizabeth A., Becker, Therese M., Hayward, Nicholas K., Bressac-de Paillerets, Brigitte, Mann, Graham J. and Melanoma Genetics Consortium (2003) eMelanoBase: An online locus-specific variant database for familial melanoma. Human Mutation, 21 1: 2-7. doi:10.1002/humu.10149


Author Fung, David C.Y.
Holland, Elizabeth A.
Becker, Therese M.
Hayward, Nicholas K.
Bressac-de Paillerets, Brigitte
Mann, Graham J.
Melanoma Genetics Consortium
Title eMelanoBase: An online locus-specific variant database for familial melanoma
Journal name Human Mutation   Check publisher's open access policy
ISSN 1059-7794
Publication date 2003-01
Sub-type Article (original research)
DOI 10.1002/humu.10149
Volume 21
Issue 1
Start page 2
End page 7
Total pages 6
Editor R.G.H. Cotton
H. H. Kazazian Jr.
Place of publication Hoboken, U.S.A.
Publisher John Wiley & Sons
Collection year 2003
Language eng
Subject C1
321011 Medical Genetics
730107 Inherited diseases (incl. gene therapy)
Abstract A proportion of melanoma,prone individuals in both familial and non,familial contexts has been shown to carry inactivating mutations in either CDKN2A or, rarely, CDK4. CDKN2A is a complex locus that encodes two unrelated proteins from alternately spliced transcripts that are read in different frames. The alpha transcript (exons 1a, 2, and 3) produces the p16INK4A cyclin-dependent kinase inhibitor, while the beta transcript (exons 1beta and 2) is translated as p14ARF, a stabilizing factor of p53 levels through binding to MDM2. Mutations in exon 2 can impair both polypeptides and insertions and deletions in exons 1alpha, 1beta, and 2, which can theoretically generate p16INK4A,p14ARF fusion proteins. No online database currently takes into account all the consequences of these genotypes, a situation compounded by some problematic previous annotations of CDKN2A related sequences and descriptions of their mutations. As an initiative of the international Melanoma Genetics Consortium, we have therefore established a database of germline variants observed in all loci implicated in familial melanoma susceptibility. Such a comprehensive, publicly accessible database is an essential foundation for research on melanoma susceptibility and its clinical application. Our database serves two types of data as defined by HUGO. The core dataset includes the nucleotide variants on the genomic and transcript levels, amino acid variants, and citation. The ancillary dataset includes keyword description of events at the transcription and translation levels and epidemiological data. The application that handles users' queries was designed in the model,view. controller architecture and was implemented in Java. The object-relational database schema was deduced using functional dependency analysis. We hereby present our first functional prototype of eMelanoBase. The service is accessible via the URL www.wmi.usyd.e, du.au:8080/melanoma.html.
Keyword Genetics & Heredity
Melanoma, Familial
Database
Germline Variants
Model-view-controller Architecture
Cdkn2a
Cdk4
Mutations
Risk
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2004 Higher Education Research Data Collection
School of Medicine Publications
 
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Created: Tue, 14 Aug 2007, 19:31:41 EST