National and ethnic mutation databases: recording populations' genography

Abstract

Genetic databases are gradually assuming an increasing importance in all areas of health care. The national and ethnic mutation databases (NEMDBs) are continuously updated mutation depositories, recording extensive information over the described genetic heterogeneity of an ethnic group or population. Together with the central and locus-specific databases, those resources not only enhance awareness of the various genetic disorders but also facilitate the provision of genetic services and provide useful insights into the genographic history of human populations. Fifteen independent NEMDBs devoted to the documentation of the extant genetic heterogeneity in various population groups within 57 different countries were assessed; 13 of the NEMDBs were fully functional. The contents of the 13 fully functional NEMDBs were thoroughly analyzed for the presence or absence of 39 criteria, pertaining database general information, operating platform, data source and submission, and querying capacity. This study provides a strong case for uniformity of data to make the NEMDBs content maximally useful. In this direction, a hypothetical content for the ideal NEMDB is derived, which is currently being incorporated in an upgraded version of the ETHNOS NEMDB development and curation software, as well as a community structure that would enhance the chances of mutation frequency capture and documentation in human populations. The ultimate goal is that interested parties and granting bodies will assist in achieving the vision of a comprehensive resource that collects and displays all population-specific genetic information discovered.

Initiating a Human Variome Project Country Node

“…There has also been a review of the earlier activities [Patrinos, 2006]. Each of these accomplishments is a success in demonstrating the feasibility of the Human Variome Project model of collection.…”

Documentation of inherited disorders and mutation frequencies in the different religious communities in Israel in the Israeli National Genetic Database

“…The ETHNOS software is a flat-file database management system, which was specifically developed to allow uniform NEMDB construction and curation. This software has initially supported the construction of five different NEMDBs [Patrinos, 2006]. However, to fulfill the requirements of the existing datasets related to the genetic disorders of the Israeli populations, the software has been modified to cope not only with easy and secure (password-protected) data entry, storage, and curation of the large datasets requiring documentation, but also to address a number of novel features that would make the database appeal to a larger user group.…”

“…It is noteworthy that the ETHNOS software, upgraded for the construction of the Israeli NEMDB, has maintained its flat-file database management functionalities and is different from the one supporting the FINDbase operation, which is MySQL-based (www.mysql.com; Uppsala, Sweden) and has relational, and hence more advanced, database management properties. Nevertheless, although the rest (non-ETHNOS-based) of the NEMDBs are operating using a relational database management system [Patrinos, 2006] (see also Table 1), they lack a number of features included in the much simpler flat-file ETHNOS software, supporting the Israeli NEMDB (see also below).…”

“…NEMDBs are becoming increasingly important for the provision of genetic services and documentation of population ''genography'' [Patrinos, 2006]. The ETHNOS database platform, exclusively designed to facilitate the construction of NEMDBs, has contributed to the promotion of the establishment of similar databases from different countries and also to database uniformity, as more than half of the available NEMDBs are based on this platform.…”

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility

“…4 NEMDBs record mutation spectrum observed in a particular population or ethnic group; they provide relevant information to study the population origin and migration flow. 5 The Human Genome Variation Society (HGVS) maintains comprehensive and updated lists of LSDBs and NEMDBs, in a dedicated website (http://www.hgvs.org), which presents guidelines and recommendations to generate the content and structure of variation databases. The HGVS website displays two mutation databases dedicated to the Arab population, including the Catalogue of Transmission Genetics in Arabs (CTGA) Database, constructed by the Centre for Arab Genomic Studies, and The Lebanese National Mutation Frequency Database.…”