Eye disorder database "KMeyeDB"

'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, ‘RetinoGenetics’, which contains informative knowledge about all known IRD-related genes and mutations for IRD. ‘RetinoGenetics’ currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein–protein interaction, mutational annotations and gene–disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, ‘RetinoGenetics’ could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, ‘RetinoGenetics’ is an integrative, informative and updatable resource for IRD-related genetic predispositions.

Database URL:http://www.retinogenetics.org/.

KMeyeDB: a graphical database of mutations in genes that cause eye diseases

KMeyeDB (http://mutview.dmb.med.keio.ac.jp/) is a database of human gene mutations that cause eye diseases. We have substantially enriched the amount of data in the database, which now contains information about the mutations of 167 human genes causing eye-related diseases including retinitis pigmentosa, cone-rod dystrophy, night blindness, Oguchi disease, Stargardt disease, macular degeneration, Leber congenital amaurosis, corneal dystrophy, cataract, glaucoma, retinoblastoma, Bardet-Biedl syndrome, and Usher syndrome. KMeyeDB is operated using the database software MutationView, which deals with various characters of mutations, gene structure, protein functional domains, and polymerase chain reaction (PCR) primers, as well as clinical data for each case. Users can access the database using an ordinary Internet browser with smooth user-interface, without user registration. The results are displayed on the graphical windows together with statistical calculations. All mutations and associated data have been collected from published articles. Careful data analysis with KMeyeDB revealed many interesting features regarding the mutations in 167 genes that cause 326 different types of eye diseases. Some genes are involved in multiple types of eye diseases, whereas several eye diseases are caused by different mutations in one gene.

EyeSite: a semi-automated database of protein families in the eye

The EyeSite is a web-based database of protein families for proteins that function in the eye and their homologous sequences. The resource clusters proteins at different levels of homology in order to facilitate functional annotation of sequences and modelling of proteins from structural homologues. Eye proteins are organized into the tissue types in which they function and are clustered into homologous families using a novel protocol employing the TribeMCL algorithm. Homologous families are further subdivided into sequence clusters for which multiple sequence alignments are generated. Structural annotations from the CATH domain database are provided for nearly 90% of the sequences, and protein family annotations from the Pfam database for approximately 86%. Homology models have also been generated where appropriate. The EyeSite is stored in a relational database and is extensively linked to other online bioinformatics resources to help relate allelic variants, annotations and clinical details to the derived data in the database. The EyeSite is available for online search, sequence information and model retrieval at http://eyesite.cryst.bbk.ac.uk/.

Time for a unified system of mutation description and reporting: a review of locus-specific mutation databases

Mutation databases of human genes are assuming an increasing importance in all areas of health care. In addition, more and more experts in the mutations and diseases of particular genes are curating published and unpublished mutations in locus-specific databases (LSDB). These databases contain such extensive information that they have become known as knowledge bases. We analyzed these databases and their content between June 21, 2001, and July 18, 2001. We were able to access 94 independent websites devoted to the documentation of mutation containing 262 LSDBs for study. We analyzed one LSDB from each of these websites (i.e., 94 LSDBs) for the presence or absence of 80 content criteria, as generally each gene in a multigene website documented the same criteria. No criterion studied gave unanimous agreement in every database. Twenty-two genes were represented by more than one LSDB. The number of mutations recorded, excluding p53, was 23,822 with 1518 polymorphisms. Fifty-four percent of the LSDBs studied were easy to use and 11% hard to follow; 73% of the databases were displayed through HTML. Three databases were found that were given a high score for ease of use and wealth of content. Thus, the study provided a strong case for uniformity of data to make the content maximally useful. In this direction, a hypothetical content for an ideal LSDB was derived. We also derived a community structure that would enhance the chances of mutation capture rather than being left unpublished in a patient's report. We hope the interested community and granting bodies will assist in achieving the vision of a public system that collects and displays all variants discovered.

Differential occurrence of mutations causative of eye diseases in the Chinese population

Ethnic differences and geographic variations affect the frequencies and nature of human mutations. In the literature, descriptions of causative mutations of eye diseases in the Chinese population are few. In this paper we attempt to reveal molecular information on genetic eye diseases involving Chinese patients from published and unpublished works by us and other groups. Our studies on candidate genes of eye diseases in the Chinese population in Hong Kong include MYOC and TISR for primary open angle glaucoma, RHO and RP1 for retinitis pigmentosa, ABCA4 and APOE for age-related macular degeneration, RB1 for retinoblastoma, APC for familial adenomatous polyposis with congenital hypertrophy of retinal pigment epithelium, BIGH3/TGFBI for corneal dystrophies, PAX6 for aniridia and Reiger syndrome, CRYAA and CRYBB2 for cataracts, and mtDNA for Leber hereditary optic neuropathy. We have revealed novel mutations in most of these genes, and in RHO, RP1, RB1, BIGH3, and PAX6 we have reported mutations that contribute to better understanding of the functions and properties of the respective gene products. We showed absence of MYOC does not necessarily cause glaucoma. No disease causative mutations have been identified in MYOC or ABCA4. There are similarities in the patterns of sequence alterations and phenotype-genotype associations in comparison with other ethnic groups, while the MYOC, RB1, APC, and PAX6 genes have more Chinese-specific sequence alterations. Establishment of a mutation database specific for the Chinese is essential for identification of genetic markers with diagnostic, prognostic, or pharmacological values.

7th International HUGO Mutation Database Meeting, October 19, 1999, San Francisco, USA

The 7th International HUGO Mutation Database Meeting was held on October 19, 1999 in conjunction with the annual meeting of the American Society of Genetics in San Fransisco, California, U.S.A. Meeting highlights are described, including discussions of topics such as the ethical aspects of variation databases, ethical guidelines which should be established immediately, data protection laws which may affect access to data, and plans to make variation databases financially self-sustaining. A resolution was passed which encourages HUGO and Mutation database Initiative (MDI) collaboration (under the name HUGO-MDI) to provide an integrated, properly funded system of variation databases.

MuStaR and other software for locus-specific mutation databases

As the human genome sequencing project nears completion, there has been a vast increase in the rate at which disease and nondisease associated variant sequences are being sought and detected. This has heightened the need for software with which to accumulate allelic variant (mutation) data, and with which to make the data accessible to the scientific community. Many ad hoc solutions have been developed by those interested in specific genes and diseases, and the creation of central databases which hold data for all genes has provided an alternative repository for some of the locus data. Despite this, few specialised software tools exist for researchers to create their own locus-specific allelic variant databases. This article describes methods available to potential curators, including software systems developed with the sole purpose of generating locus-specific mutation databases. In particular, the authors' own software, MuStaRtrade mark, is described. MuStaRtrade mark allows curators to maintain a database on a laptop computer if desired, while being able to export the data to an automatically generated Website which will run on any cgi compliant Web server. Searching the database and the submission of new mutations are made possible through fill-in Web forms. A number of other software tools which may be of use to curators are also described.

Guidelines and recommendations for content, structure, and deployment of mutation databases: II. Journey in progress

The HUGO Mutation Database Initiative has produced guidelines and recommendations addressing uniform nomenclature of (human) genes and alleles, and computing standards to permit a moderate level of built-in redundancy, searchable interfaces, and compatibility between the comprehensive (genomic) and locus-specific types of databases. The participating community (developers and users) have been moving the project along rapidly, as described here.