A1ATVar: A relational database of human SERPINA1 gene variants leading to α1-antitrypsin deficiency and application of the VariVis software
Human Mutation , Volume 30 - Issue 3 p. 308- 313
We have developed a relational database of human SERPINA1 gene mutations, leading to α1-antitrypsin (AAT) deficiency, called A 1ATVar, which can be accessed over the World Wide Web at www.goldenhelix.org/A1ATVar. Extensive information has been extracted from the literature and converted into a searchable database, including genotype information, clinical phenotype, allelic frequencies for the commonest AAT variant alleles, methods of detection, and references. Mutation summaries are automatically displayed and user-generated queries can be formulated based on fields in the database. A separate module, linked to the FINDbase database for frequencies of inherited disorders allows the user to access allele frequency information for the three most frequent AAT alleles, namely PiM, PiS, and PiZ. The available experimental protocols to detect AAT variant alleles at the protein and DNA levels have been archived in a searchable format. A visualization tool, called VariVis, has been implemented to combine A 1ATVar variant information with SERPINA1 sequence and annotation data. A direct data submission tool allows registered users to submit data on novel AAT variant alleles as well as experimental protocols to explore SERPINA1 genetic heterogeneity, via a password-protected interface. Database access is free of charge and there are no registration requirements for querying the data. The A1ATVar database is the only integrated database on the Internet offering summarized information on AATallelic variants and could be useful not only for clinical diagnosis and research on AAT deficiency and the SERPINA1 gene, but could also serve as an example for an all-in-one solution for locus-specific database (LSDB) development and curation. © 2008 Wiley-Liss, Inc.
|AAT, DNA, Experimental protocols, Internet, Mutations, Populations, Relational database, SERPINA1, SERPINA1 protein, Visualization tool, allele, alpha 1 antitrypsin, alpha 1 antitrypsin deficiency, article, computer program, data base, gene frequency, gene mutation, genetic database, genetic heterogeneity, genetic variability, genetics, genotype, human, medical information, medical literature, mutation, neuroserpin, nucleotide sequence, pathology, phenotype, priority journal, α1-antitrypsin deficiency|
|Organisation||Erasmus MC: University Medical Center Rotterdam|
Zaimidou, S, van Baal, S, Smith, T.D, Mitropoulos, K, Ljujic, M, Radojkovic, D, … Patrinos, G.P. (2009). A1ATVar: A relational database of human SERPINA1 gene variants leading to α1-antitrypsin deficiency and application of the VariVis software. Human Mutation, 30(3), 308–313. doi:10.1002/humu.20857