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. 2007 Jan;35(Database issue):D690-5.
doi: 10.1093/nar/gkl934. Epub 2006 Nov 28.

FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide

Sjozef van Baal  1 , Polynikis Kaimakis, Manyphong Phommarinh, Daphne Koumbi, Harry Cuppens, Francesca Riccardino, Milan Macek Jr, Charles R Scriver, George P Patrinos
Affiliations

FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide

Sjozef van Baal et al. Nucleic Acids Res. 2007 Jan.

Abstract

Frequency of INherited Disorders database (FINDbase) (http://www.findbase.org) is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders worldwide. Database records include the population and ethnic group, the disorder name and the related gene, accompanied by links to any corresponding locus-specific mutation database, to the respective Online Mendelian Inheritance in Man entries and the mutation together with its frequency in that population. The initial information is derived from the published literature, locus-specific databases and genetic disease consortia. FINDbase offers a user-friendly query interface, providing instant access to the list and frequencies of the different mutations. Query outputs can be either in a table or graphical format, accompanied by reference(s) on the data source. Registered users from three different groups, namely administrator, national coordinator and curator, are responsible for database curation and/or data entry/correction online via a password-protected interface. Databaseaccess is free of charge and there are no registration requirements for data querying. FINDbase provides a simple, web-based system for population-based mutation data collection and retrieval and can serve not only as a valuable online tool for molecular genetic testing of inherited disorders but also as a non-profit model for sustainable database funding, in the form of a 'database-journal'.

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Figures

Figure 1
Figure 1
Querying FINDbase for frequencies of mutations leading to inherited disorders in a certain population. (a) The world map in the Home page, from where the user can quickly select the desired population to query upon by clicking on a country's capital (in this case, Hungary). A communication box automatically appears containing the corresponding national flag and the number of disorders currently documented in FINDbase. (b) Construction of the query ‘Find all inherited disorders in the Hungarian population’. Only parts of the Search page are shown. The user needs either to click on Hungary's capital from the world map (as previously described) or to select for the ‘Hungarian’ population from the population list, located either in the Home page [next to the world map (Supplementary Figure)] or at the left part of the Search page. Query results are in a table format, indicating the disorder, the gene found mutated and the mutations in their official nomenclature. (c) Construction of the query ‘Find all mutations leading to β-thalassemia in the Hungarian population’. By selecting ‘Hungarian’ and ‘Beta-thalassemia’ from the population and disorder's list respectively, the query returns a list of all β-thalassemia mutations found in the Hungarian population together with their frequencies and data source in a table (by selecting the ‘Show results as table’ button) or graphical format (by selecting the ‘Show results as chart’ button). The disorder and gene names and OMIM ID are hyperlinked to further information in the OMIM central database. (d) Sample query ‘Find all mutations leading to Cystic Fibrosis in the Austrian population with a frequency range of 1% and above’. By selecting ‘Austrian’ and ‘Cystic Fibrosis’ from the population and disorder's list respectively and specifying the desired frequency range in the corresponding boxes (indicated with an arrow), the query returns a list of all CFTR mutations with a frequency range of 1% and above found in the Austrian population together with their data source in a table or graphical format. In the latter case, the different CFTR mutation frequencies found in different geographical regions are differentially displayed, with the corresponding mutation frequencies shown in the bars.
Figure 2
Figure 2
Querying FINDbase for frequencies of mutations leading to a certain inherited disorder in different populations. (a) Construction of the query ‘Find frequent (between 2 and 100%) familial hypercholesterolemia mutations in all populations’. (b) The user needs to select for the ‘Familiar hypercholesterolemia’ disorder from the disorder's menu, located either in the Home page [next to the world map (Supplementary Figure)] or at the right part of the Search page. Query results are in a table format, indicating the populations and ethnic groups (if applicable) where LDLR mutations are found. Information is accompanied by the data source. (c) Construction of the query ‘Find the frequency of the p.S188F mutation leading to Glucose 6P-Dehydrogenase (G6PD) deficiency in all populations’. By selecting ‘Glucose 6P-Dehydrogenase deficiency’ from the disorder's list and ‘p.S188F’ from the mutation's list, the query returns a list of populations in which the p.S188F mutation is found together with the corresponding frequencies. Query output can be in a graphical (d) or table format (e), always accompanied by the data source.
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