Hellenic National Mutation Database: a prototype database for mutations leading to inherited disorders in the Hellenic population

Patrinos, George P.; Baal, Sjozèf van; Petersen, Michael B.; Papadakis, Manoussos N.

doi:10.1002/humu.20157

Cited by 48 publications

(34 citation statements)

References 36 publications

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“…We hope that the annotations will be widely used in LSDBs such as IDbases (Piirilä et al 2006) and also in some central variation databases. Other possible users include, e.g., specific variation effect databases such as ProThem and ProNIT (Kumar et al 2006), allele frequency databases like FINDbase (van Baal et al 2007), and ethnic and/or national databases like the Hellenic National Mutation Database (Patrinos et al 2005).…”

Section: Applicationsmentioning

confidence: 99%

Variation Ontology for annotation of variation effects and mechanisms

Vihinen

2013

Genome Res.

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Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) was developed to allow the annotation of effects, consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence, reference-state property, activity, etc.) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes, whether of genetic or nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism.

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Section: Applicationsmentioning

confidence: 99%

Variation Ontology for annotation of variation effects and mechanisms

Vihinen

2013

Genome Res.

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“…They are built using a custom-made PHP script that comprises the database's core engine, not only for menus and basic screens that display and parse files, but also for handling data querying. XPRbase is a flat-file database, derived from the ETHNOS V1.0 software, which facilitates the establishment of National Mutation Frequency databases (Patrinos et al, 2005b). A user guide provides some brief information on the operation and querying principles of XPRbase.…”

Section: Xprbase a Human Globin Gene Mutation Screening Protocols Damentioning

confidence: 99%

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update

et al. 2007

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Communicated by Stylianos E. AntonarakisHbVar (http://globin.bx.psu.edu/hbvar) is a locus-specific database (LSDB) developed in 2001 by a multi-center academic effort to provide timely information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology, and ethnic occurrence, accompanied by mutation frequencies and references. In addition to the regular updates to entries, we report significant advances and updates, which can be useful not only for HbVar users but also for other LSDB development and curation in general. The query page provides more functionality but in a simpler, more user-friendly format and known single nucleotide polymorphisms in the human α-and β-globin loci are provided automatically. Populationspecific β-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported δ-and α-thalassemia mutation frequency data from 10 population groups have also been incorporated. In addition, an independent flat-file database, named XPRbase (http://www.goldenhelix.org/xprbase), has been developed and linked to the main HbVar web page to provide a succinct listing of 51 experimental protocols available for globin gene mutation screening. These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype.

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“…Major disadvantages are the many incomplete fields for various disorders and/or genes (partly justified from the project's short lifespan) and the lack of mutation frequency information. The ETHNOS-based NEMDBs, namely the Hellenic [Patrinos et al, 2005b], Cypriot, Iranian [Kleanthous et al, 2006], Lebanese [Megarbane et al, 2006], and Serbian National Mutation Frequency Databases, report the frequencies of mutant alleles responsible for several inherited disorders in those populations. In addition to compiled information on each disorder (the gene involved, diagnosis, and treatment), mutation frequency data are provided, accompanied by links to OMIM and LSDBs where possible (Supplementary Figure S1).…”

Section: General Impression and Comparison Between The Existing Nemdbsmentioning

confidence: 99%

“…The system should also automatically provide the date from the last NEMDB update and a counter, set up to count each individual ''user'' visit per day only once. Unlike the recent attempts to create such software for LSDBs (MUTbase [http://bioinf.uta.fi/MUTbase/], Riikonen and Vihinen [1999]), UMD (www.umd.be) [Beroud et al, 2000], MuStaR (www.hgu.mrc.ac.uk/softdata/Mustar/) [Brown and McKie, 2000], LOVD (www.dmd.nl/LOVD/1.1.0/) [Fokkema et al, 2005], the ETHNOS software is the only specialized NEMDB construction and maintenance software, and it only emerged recently [Patrinos et al, 2005b]. Although simple in concept and design, it holds promise for a more uniform and useful set of this type of databases.…”

Section: Toward a Model Nemdbmentioning

confidence: 99%

National and ethnic mutation databases: recording populations' genography

Patrinos

2006

Hum. Mutat.

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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.

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Hellenic National Mutation Database: a prototype database for mutations leading to inherited disorders in the Hellenic population

Cited by 48 publications

References 36 publications

Variation Ontology for annotation of variation effects and mechanisms

Variation Ontology for annotation of variation effects and mechanisms

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update

National and ethnic mutation databases: recording populations' genography

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