ETHNOS : A versatile electronic tool for the development and curation of national genetic databases
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ETHNOS: A versatile electronic tool for the development and curation of national genetic databases Sjozef van Baal,1 Joe¨l Zlotogora,2 George Lagoumintzis,3,4 Vassiliki Gkantouna,5 Ioannis Tzimas,5 Konstantinos Poulas,3 Athanassios Tsakalidis,5 Giovanni Romeo6 and George P. Patrinos3* 1
Erasmus MC, Faculty of Medicine and Health Sciences, MGC-Department of Cell Biology and Genetics, Rotterdam 3015CE, the Netherlands 2 Department of Community Genetics, Public Health Services, Ministry of Health, Ramat Gan, 52621, Israel 3 Department of Pharmacy, School of Health Sciences, University of Patras, Patras, 26504, Greece 4 Department of Optics and Optometry, Technological Educational Institute of Patras, Patras, 26334, Greece 5 University of Patras, Faculty of Engineering, Department of Computer Engineering and Informatics, Patras, 26504, Greece 6 Unita` di Genetica Medica, Policlinico Universitario S. Orsola-Malpighi, Bologna, 40138, Italy *Correspondence to: Tel/Fax: þ30 2610 969834; E-mail: [email protected] Date received (in revised form): 22 April 2010
Abstract National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation. Keywords: genetic disorders, database, software, mutations, laboratories
Introduction In recent years, advances in our understanding of genotype – phenotype correlations and the evolution of genomics technology and nanotechnology have resulted in the generation of enormous amounts of genetic data. These data are usually stored in genetic databases, namely data repositories
for genome variation data and their phenotypic consequences. Genetic databases can be categorised into three types: (1) General (core) mutation databases (GMDBs); (2) locus-specific databases (LSDBs) and (3) national and ethnic mutation databases (NEMDBs).1 GMDBs attempt to
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