The genetic association database.
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Databases, Genetic↗
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Arab genetic disease database (AGDDB): a population-specific clinical and mutation database.
Here we present the Arab Genetic Disease Database (AGDDB), a curated catalog of genetic disorders found in Arab populations. The first release of the database is populated primarily with information from the textbook Genetic Disorders Among Arab Populations [Teebi and Farag, 1997]. AGDDB is composed of data elements revolving around disorder reports. Other reports cover clinical, genomic, reference, and population frequency elements and their important attributes. The Arab Genetic Disease Consortium (30 investigators, 18 countries) is responsible for editing and reviewing AGDDB data. After initial indexing, AGDDB contains over 1,000 unique disorder entries. Entries are linked to their counterparts in the Online Mendelian Inheritance in Man (OMIM) database; similar associations with relevant locus-specific and central mutation databases are planned. The database can be queried by keyword across all its fields, with more focused searches allowed. The database is freely available and may be accessed at www.agddb.org. The database serves as a robust prototype for cataloging variation and disorder information within a specific population.
Arabs↗
CTGA: the database for genetic disorders in Arab populations.
The Arabs comprise a genetically heterogeneous group that resulted from the admixture of different populations throughout history. They share many common characteristics responsible for a considerable proportion of perinatal and neonatal mortalities. To this end, the Centre for Arab Genomic Studies (CAGS) launched a pilot project to construct the 'Catalogue of Transmission Genetics in Arabs' (CTGA) database for genetic disorders in Arabs. Information in CTGA is drawn from published research and mined hospital records. The database offers web-based basic and advanced search approaches. In either case, the final search result is a detailed HTML record that includes text-, URL- and graphic-based fields. At present, CTGA hosts entries for 692 phenotypes and 235 related genes described in Arab individuals. Of these, 213 phenotypic descriptions and 22 related genes were observed in the Arab population of the United Arab Emirates (UAE). These results emphasize the role of CTGA as an essential tool to promote scientific research on genetic disorders in the region. The priority of CTGA is to provide timely information on the occurrence of genetic disorders in Arab individuals. It is anticipated that data from Arab countries other than the UAE will be exhaustively searched and incorporated in CTGA (http://www.cags.org.ae).
Arabs↗
Human exposures to mutagens--an analysis using the genetic activity profile database.
The Genetic Activity Profile (GAP) database was used to identify and compare agents showing genotoxic activity in humans. The database revealed several substances for which both human and rodent cytogenetic data existed. Based on the ratio of the lowest effective doses (LEDs) in rodents versus human studies, humans appear to be at least 10 times more sensitive than rodents to the majority of the genotoxic substances examined. Several caveats are discussed which may be responsible, in part, for the apparent differences in sensitivity. Some of these differences could be due to variations in the test protocols or they may, in fact, reflect real differences between human and rodent cells. However, in contrast to the in vivo comparison, the LEDs for human data from in vitro studies were not uniformly lower than for comparable studies in rodents. The in vitro comparison suggests that the apparent differences in human versus rodent cell sensitivity seen in vivo must be viewed with a degree of caution. Nevertheless, the overall GAPs for these agents, and particularly the human in vivo data, underscore the concern for adequate protection of humans exposed to these environmental mutagens.
Animals↗
Prototyping a genetics deductive database.
We are developing a laboratory notebook system known as the Genetics Deductive Database. Currently our prototype provides storage for biological facts and rules with flexible access via an interactive graphical display. We have introduced a formal basis for the representation and reasoning necessary to order genome map data and handle the uncertainty inherent in biological data. We aim to support laboratory activities by introducing an experiment planner into our prototype. The Genetics Deductive Database is built using new database technology which provides an object-oriented conceptual model, a declarative rule language, and a procedural update language. This combination of features allows the implementation of consistency maintenance, automated reasoning, and data verification.
Animals↗
"Iceland Inc."?: On the ethics of commercial population genomics.
A detailed analysis of the Icelandic commercial population-wide genomics database project of deCODE Genetics was performed for the purpose of providing ethics insights into public/private efforts to develop genetic databases. This analysis examines the moral differences between the general case of governmental collection of medical data for public health purposes and the centralized collection planned in Iceland. Both the process of developing the database and its design vary in significant ways from typical government data collection and analysis activities. Because of these differences, the database may serve the interests of deCODE more than it serves the interests of the public, undermining the claim that presumed consent for this data collection and its proprietary use is ethical. We believe that there is an evolving consensus that informed consent of participants must be secured for population-based genetics databases and research. The Iceland model provides an informative counterexample that holds key ethics lessons for similar ventures.
Databases, Genetic↗
Development of a national genetic services database.
The Council of Regional Networks for Genetics Services (CORN) designed and developed a database collection project to collect minimum data regarding genetic services provided throughout the United States. The data collection project has been designed to improve the provision of services and to determine areas of utilization.
Databases, Factual↗
The genetic toxicity database of the National Toxicology Program: evaluation of the relationships between genetic toxicity and carcinogenicity.
The database of the U.S. National Toxicology Program has been developed over approximately two decades, principally focused on substances evaluated for carcinogenicity in rodent bioassays. These assays generally provide data on the relative toxicity and carcinogenicity of chemicals based upon discrete subchronic (13 week) and chronic (104 week) exposures. A major value of these data are that the assay protocols, rodent strains, and technical methodologies have been generally consistent, thus permitting comparisons between assays and chemicals. The genotoxicity data for many of the same chemicals have been developed also using standardized biological systems and protocols. Data for assays including mutagenicity in Salmonella and mouse lymphoma cells, chromosomal aberrations, and sister chromatid exchange in Chinese hamster ovary cells, transformation of Balb/c 3T3 cells, and in vivo cytogenetic effects in rodents have been compiled for many chemicals. The results of all of these assays provide a substantial database for evaluating chemical effects and for defining the complex relationships between mutagenicity and carcinogenicity.
Animals↗
The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group.
The Mouse Genome Database (MGD) focuses on the integration of mapping, homology, polymorphism and molecular data about the laboratory mouse. Detailed descriptions of genes including their chromosomal location, gene function, disease associations, mutant phenotypes, molecular polymorphisms and links to representative sequences including ESTs are integrated within MGD. The association of information from experiment to gene to genome requires careful coordination and implementation of standardized vocabularies, unique nomenclature constructions, and detailed information derived from multiple sources. This information is linked to other public databases that focus on additional information such as expression patterns, sequences, bibliographic details and large mapping panel data. Scientists participate in the curation of MGD data by generating the Chromosome Committee Reports, consulting on gene family nomenclature revisions, and providing descriptions of mouse strain characteristics and of new mutant phenotypes. MGD is accessible at http://www.informatics.jax.org
Animals↗
Governing UK Biobank: the importance of ensuring public trust.
In the autumn of 2003, UK Biobank published the first draft of its Ethics and Governance Framework. Subsequently, this document has been available for interested parties to comment on and the UK Biobank Board of Directors is expected to adopt the final version in 2004. Here, we aim to contribute to this process and highlight to a wider audience some of the inconsistencies in the issues of consent, governance and right of withdrawal that emerge from the draft of the Framework. These issues will have implications for securing the public trust and long-term support that the success of the project depends on. Therefore, they must be considered carefully because the UK Biobank will be the first ever genetic database of a general population of this size to become operational, and will be used as a model for other projects of this kind.
Biological Specimen Banks↗
Thesaurus-based disambiguation of gene symbols.
BACKGROUND: Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck. RESULTS: We developed a simple thesaurus-based disambiguation algorithm that can operate with very little training data. The thesaurus comprises the information from five human genetic databases and MeSH. The extent of the homonym problem for human gene symbols is shown to be substantial (33% of the genes in our combined thesaurus had one or more ambiguous symbols), not only because one symbol can refer to multiple genes, but also because a gene symbol can have many non-gene meanings. A test set of 52,529 Medline abstracts, containing 690 ambiguous human gene symbols taken from OMIM, was automatically generated. Overall accuracy of the disambiguation algorithm was up to 92.7% on the test set. CONCLUSION: The ambiguity of human gene symbols is substantial, not only because one symbol may denote multiple genes but particularly because many symbols have other, non-gene meanings. The proposed disambiguation approach resolves most ambiguities in our test set with high accuracy, including the important gene/not a gene decisions. The algorithm is fast and scalable, enabling gene-symbol disambiguation in massive text mining applications.
Algorithms↗
Congenital and idiopathic scoliosis: clinical and genetic aspects.
OBJECTIVE: Genetic and environmental factors influencing spinal development in lower vertebrates are likely to play a role in the abnormalities associated with human congenital scoliosis (CS) and idiopathic scoliosis (IS). An overview of the molecular embryology of spinal development and the clinical and genetic aspects of CS and IS are presented. Utilizing synteny analysis of the mouse and human genetic databases, likely candidate genes for human CS and IS were identified. DESIGN: Review and synteny analysis. METHODS: A search of the Mouse Genome Database was performed for "genes," "markers" and "phenotypes" in the categories Neurological and neuromuscular, Skeleton, and Tail and other appendages. The Online Mendelian Inheritance in Man was used to determine whether each mouse locus had a known human homologue. If so, the human homologue was assigned candidate gene status. Linkage maps of the chromosomes carrying loci with possibly relevant phenotypes, but without known human homologues, were examined and regions of documented synteny between the mouse and human genomes were identified. RESULTS: Searching the Mouse Genome Database by phenotypic category yielded 100 mutants of which 66 had been mapped. The descriptions of each of these 66 loci were retrieved to determine which among these included phenotypes of scoliosis, kinky or bent tails, other vertebral abnormalities, or disturbances of axial skeletal development. Forty-five loci of interest remained, and for 27 of these the comparative linkage maps of mouse and human were used to identify human syntenic regions to which plausible candidate genes had been mapped. CONCLUSION: Synteny analysis of mouse candidate genes for CS and IS holds promise due to the close evolutionary relationship between mice and human beings. With the identification of additional genes in animal model systems that contribute to different stages of spine development, the list of candidate genes for CS and IS will continue to grow.
Animals↗
[System of distributed storage and analysis of genomic information].
A distributed computing system is developed to search and analyze genetic databases using parallel computing technologies. Queries are processed by a local network PC cluster. A universal task and data exchange format is developed for effective query processing. A multilevel hierarchic task batching procedure is elaborated to generate multiple subtasks and distribute them over cluster units under dynamic priority levels and with dynamic distribution of replicated source data subbases. Primary source data preparation and generation of annotation word indices are used to significantly reduce query processing time.
Databases, Genetic↗
[Genetic information database].
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Chromosome Mapping↗
A database of genetically determined neurological conditions for clinicians.
Progress is reported in the establishment of a database of genetically determined neurological conditions. There are now 1,300 conditions and 3,400 references store on the hard disk of a microcomputer. The database is searched, and a differential diagnosis obtained, by choosing a small number of signs and symptoms from a comprehensive list of cardinal features.
Diagnosis, Computer-Assisted↗
The Southwest of Scotland Structural Chromosomal Abnormalities Database: an assessment of its contribution to genetic counselling in affected families.
AIM: To assess the effect of establishing a genetic database on the provision of genetic counselling to individuals and families with structural chromosomal abnormalities. METHOD: For the four year period 1997-2000, we compared all cytogenetics laboratory records with entries on the database to determine its completeness. We assessed the extent to which families had been followed up, compared these findings with a previous four year period (1977-1980) and sought to discover why some families were not followed up. RESULTS: Of 215 probands identified during 1997-2000, 19 (9%) were not recorded on the register. Approximately one third of families were followed up completely, one third were partially followed up and one third had had no follow-up, for a variety of reasons. In this last group, there was evidence that some had received inadequate or incorrect genetic advice. There was no evidence that the database improved follow-up in families with structural chromosome abnormalities. Over 20 years, there has been a downward trend in the proportion of cases referred to the genetic clinic. CONCLUSIONS: Our register can be used to monitor trends in clinical practice but has had no direct effect on the service provided to patients and their families.
Chromosome Aberrations↗
[Database for genetic resource information].
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Animals↗
Implementation of a classification hierarchy for the GeneTests/GeneClinics genetic testing databases.
The combination of a) our changing understanding of genotypic and phenotypic classification of diseases and b) the rapid growth and expansion of the number of entries in two databases targeted toward clinicians resulted in the need to develop a flexible dynamic hierarchical classification system for genetic disorders. The two databases making use of this classification schemas are the GeneClinics (GC) database - www.geneclinics.org and the GeneTests (GT) database - www.genetests.org The GC and GT databases serve respsectively as the users manual and yellow pages of genetic testing. The GeneTests/GeneClinics (GT/GC) classification hierarchy is maintained as a simple set of parent/child relationships in a relational database. The hierarchy is generated in real time in response to a user request. It is not maintained as a set of members with relationships defined by characters that are parsed to determine the structure of the tree. The GT/GC classification hierarchy entries are handled as objects by the data maintenance and search tools and may have a number of attributes and associations that create a rich tool for defining and examining genetic disorders
Databases, Genetic↗