A database of locus-specific databases

Horaitis, Ourania; Talbot, C. Conover; Phommarinh, Manyphong; Phillips, Kate M.; Cotton, Richard G.H.

doi:10.1038/ng0407-425

Cited by 52 publications

(37 citation statements)

References 16 publications

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“…Sadly, the resulting flood of primary genomic information is not yet being managed or utilized as effectively as it should be, due, not least, to the lack of a sufficiently organized and mature database infrastructure. Two international consortia have emerged to assist in addressing these issues, namely, the Human Variome Project (HVP; http://www.human variomeproject.org) [Horaitis et al, 2007;Kaput et al, 2009] and the GEN2PHEN project (http://www.gen2phen.org), an integrated project funded by the European Commission.…”

Section: Discussionmentioning

confidence: 99%

Locus-specific database domain and data content analysis: evolution and content maturation toward clinical usea

et al. 2010

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Genetic variation databases have become indispensable in many areas of health care. In addition, more and more experts are depositing published and unpublished disease-causing variants of particular genes into locus-specific databases (LSDBs). Some of these databases contain such extensive information that they have become known as knowledge bases. Here, we analyzed 1,188 LSDBs and their content for the presence or absence of 44 content criteria related to database features (general presentation, locus-specific information, database structure) and data content (data collection, summary table of variants, database querying). Our analyses revealed that several elements have helped to advance the field and reduce data heterogeneity, such as the development of specialized database management systems and the creation of data querying tools. We also identified a number of deficiencies, namely, the lack of detailed disease and phenotypic descriptions for each genetic variant and links to relevant patient organizations, which, if addressed, would allow LSDBs to better serve the clinical genetics community. We propose a structure, based on LSDBs and closely related repositories (namely, clinical genetics databases), which would contribute to a federated genetic variation browser and also allow the maintenance of variation data.

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Section: Discussionmentioning

confidence: 99%

Locus-specific database domain and data content analysis: evolution and content maturation toward clinical usea

et al. 2010

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“…The first of these 'Locus-Specific Databases' (LSDBs) was published in 1976, in the form of a catalog of human globin mutations 15 . Following a slow but steady increase in the number of online LSDBs, ~700 are now listed at the Human Genome Variation Society website 16 (http://www.hgvs.org/dblist/glsdb.html). LSDB entries tend to be rich in information content and enhanced by domain-specific expert curation.…”

Section: Locus-specific Databases For Human 'Mendelian Mutations'mentioning

confidence: 99%

Genotype–phenotype databases: challenges and solutions for the post-genomic era

2009

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“…This knowledge will be accessible to the research and medical communities to improve research strategies and clinical medical practice. One of the key deliverables of the HVP is the creation of a cyber infrastructure to link locus-specific databases (LSDBs [27]). These databases have similar architecture, ontologies, and data elements allowing for interoperability and are curated by local experts.…”

Section: The Human Variome Projectmentioning

confidence: 99%

Connecting the Human Variome Project to nutrigenomics

et al. 2010

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Nutrigenomics is the science of analyzing and understanding gene-nutrient interactions, which because of the genetic heterogeneity, varying degrees of interaction among gene products, and the environmental diversity is a complex science. Although much knowledge of human diversity has been accumulated, estimates suggest that *90% of genetic variation has not yet been characterized. Identification of the DNA sequence variants that contribute to nutrition-related disease risk is essential for developing a better understanding of the complex causes of disease in humans, including nutrition-related disease. The Human Variome Project (HVP; http://www.humanvariomeproject. org/) is an international effort to systematically identify genes, their mutations, and their variants associated with phenotypic variability and indications of human disease or phenotype. Since nutrigenomic research uses genetic information in the design and analysis of experiments, the HVP is an essential collaborator for ongoing studies of gene-nutrient interactions. With the advent of next generation sequencing methodologies and the understanding of the undiscovered variation in human genomes, the nutrigenomic community will be generating novel sequence data and results. The guidelines and practices of the HVP can guide and harmonize these efforts.

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A database of locus-specific databases

Cited by 52 publications

References 16 publications

Locus-specific database domain and data content analysis: evolution and content maturation toward clinical usea

Locus-specific database domain and data content analysis: evolution and content maturation toward clinical usea

Genotype–phenotype databases: challenges and solutions for the post-genomic era

Connecting the Human Variome Project to nutrigenomics

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