GeneRetriever: software to extract all genes and transcripts in between two genetic markers to assist design of human custom microarrays.
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Algorithms↗
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Results for “Databases, Genetic”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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[Genetic analysis and virulence factors of group A streptococci that cause severe invasive infectious diseases].
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Adhesins, Bacterial↗
Genetic polymorphism of two STR loci D1S1609 and D18S976 in a Chinese population.
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Asian People↗
FISH: a guide to protein-coding DNA sequences in the GenBank database.
FISH (Fast Index Search for Homologous coding sequences) consists of a database and associated software and is intended to function as a directory of protein-coding gene sequences. The FISH index contains descriptions of 22,361 DNA sequences from release 69.0 of the GenBank genetic sequence database. Complete coding sequences are represented numerically with counts of nucleotides and synonymous codons, and with GenBank LOCUS names and short descriptions. The software permits the database to be queried by GenBank LOCUS name, sequence length (expressed as total number of codons), or by comparison with a DNA sequence. In the latter case, the numerical descriptions are compared with simple distance measures in place of actual DNA sequences. The FISH package can be used to rapidly assemble lists of similar coding sequences, without regard to functional annotation or sequence alignments. Typical search times are well under a minute on widely available IBM-compatible microcomputers.
Algorithms↗
Genetic dissection of the common epilepsies.
PURPOSE OF REVIEW: Only two functionally validated susceptibility genes, CACNA1H and GABRD, have so far been identified in the common epilepsies using a candidate gene approach. The difficulty with the alternative statistical approach, where none of the suggested candidates has been functionally validated, may partly be due to the posited genetic architecture of the common epilepsies, such as the idiopathic generalized epilepsies. A subset of both rare and common variants from a much larger pool of susceptibility genes may contribute to disease risk. We review methods and designs for the genetic dissection of common epilepsies. RECENT FINDINGS: Genetic association studies, though theoretically more powerful than linkage analysis, have not yet delivered validated susceptibility genes. Methodological flaws can undermine such studies but are correctable. Concerns remain, however, about the extent of underlying genetic heterogeneity in common epilepsies. Genome-wide association studies are increasingly feasible, but issues remain about their conduct and analysis. Meta-analysis may resolve conflicting association studies, facilitated by the establishment of databases of genetic association studies. Newer multi-locus and admixture mapping approaches are attractive alternatives to traditional association studies and may offer new insights into identifying epilepsy genes. SUMMARY: We conclude by emphasizing the importance of deeper endophenotyping using electroclinical, imaging, and molecular approaches to dissect the common epilepsies.
Chromosome Mapping↗
Connectivity independent protein-structure alignment: a hierarchical approach.
BACKGROUND: Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure elements (SSE) but differ in the underlying polypeptide chain connectivity (non-sequential SSE connectivity). RESULTS: We perform protein-structure alignment using a two-level hierarchical approach implemented in the program GANGSTA. On the first level, pair contacts and relative orientations between SSEs (i.e. alpha-helices and beta-strands) are maximized with a genetic algorithm (GA). On the second level residue pair contacts from the best SSE alignments are optimized. We have tested the method on visually optimized structure alignments of protein pairs (pairwise mode) and for database scans. For a given protein structure, our method is able to detect significant structural similarity of functionally important folds with non-sequential SSE connectivity. The performance for structure alignments with strictly sequential SSE connectivity is comparable to that of other structure alignment methods. CONCLUSION: As demonstrated for several applications, GANGSTA finds meaningful protein-structure alignments independent of the SSE connectivity. GANGSTA is able to detect structural similarity of protein folds that are assigned to different superfamilies but nevertheless possess similar structures and perform related functions, even if these proteins differ in SSE connectivity.
Algorithms↗
Gene testing: what the health professional needs to know.
Physicians and health professionals are faced with new challenges in the era of increasing information on genetics and health. The sequencing of the human genome has created more opportunities for genetic research and increased awareness of the role of genes in diseases. There is also an increased awareness of genetic susceptibility and gene testing. As a result of the advances in genetic research, the public demand for gene testing is on the rise. Patients are now seeking more information about inheritable diseases and predisposition to genetically related disease from doctors and other health professionals. Genetic tests are often conducted to confirm the diagnosis of a genetic disease as well as to assess genetic risk, predict response to drugs, and assist in reproductive decision making. Genetic tests are available for over 950 inherited diseases or conditions in the GeneTests data base for clinical or research purposes. A number of challenges face health professionals when using genetic tests for diagnosis, predictive testing, or reproductive decision making. These include the constant change in genetics knowledge and the increased demand to keep up with the various aspects of the genetic testing process. To meet these demands, physicians and other health professionals should use available educational genetic resources to provide adequate patient care.
Chromosome Mapping↗
The genetic cohorts: facing the new challenges in infectious diseases. The HIV model.
All physicians are confronted with the diversity of susceptibility to infectious diseases or response to medication among patients. Much work has been done to characterize the virulence factors of pathogens, while less is known about the host (human) factor. Two unrelated people share about 99.9% of their DNA sequences, while the remaining 0.1% contains the genetic variants that influence how they differ in their risk of disease or response to drugs. The completion of the Human Genome Project gives a new start to developing the field of host genetic susceptibility. This review highlights ethical and practical issues on developing genetic cohorts by using the model of the Swiss HIV Cohort Study.
Anti-HIV Agents↗
Protecting genetic materials and genetic information: a case study of Guthrie Cards in Victoria.
The authors are privileged to have been provided with correspondence about a dispute over the ongoing storage of genetic material (as Guthrie Cards) in Victoria. The correspondence details confusion over the roles of government and the private sector service provider in accounting for the storage, use and destruction of these stored genetic materials collected as part of a government public health program. The purpose in publishing this account is to highlight the present inadequacies in current practices and the ongoing potential for a crisis in the management of collected genetic materials through a lack of appropriate regulation, transparency and accountability. The article suggests measures to remedy some of the existing inadequacies in contractual arrangements and recommends that the government retain ownership and control of both the genetic materials and the derived information to ensure some accountability in the present legal environment.
Contract Services↗
[Bioethical principles concerning human genetic data].
UNESCO'S Universal declaration on the human genome and human rights (1997) has been accepted by the international scientific community. To apply these laws, it is necessary to get more specific rules about data regulation, human genetic samples and its derived information in biomedic research. Indeed, genetic material recollection, processing, use and storing, has potential risks over human rights' protection and exercise. The author, member of UNESCO'S intergovernmental Bioethics Committee which approved the final draft in June 2003, has taken part in the writing of the final text of an international declaration about human genetic data, whose abbreviate text is described and commented in this communication.
Biological Specimen Banks↗
Identification of C. elegans sensory ray genes using whole-genome expression profiling.
The three cells that comprise each C. elegans sensory ray (two sensory neurons and a structural cell) descend from a single neuroblast precursor cell. The atonal ortholog lin-32 and the E/daughterless ortholog hlh-2 act to confer neural competence during ray development, but additional regulatory factors that control specific aspects of cell fate are largely unknown. Here, we use full-genome DNA microarrays to compare gene expression profiles in adult males of two mutant strains to identify new components of the regulatory network that controls ray development and function. This approach identified a large set of candidate ray genes. Using reporter genes, we confirmed ray expression for 13 of these, including a beta-tubulin, a TWK-family channel, a putative chemoreceptor and four novel genes (the cwp genes) with a potential role in sensory signaling through the C. elegans polycystins lov-1 and pkd-2. Additionally, we have found several ray-expressed transcription factors, including the Zn-finger factor egl-46 and the bHLH gene hlh-10. The expression of many of these genes requires lin-32 function, though this requirement may not reflect direct activation by lin-32. Our strategy provides a complementary foundation for modeling the genetic network that controls the development of a simple sensory organ.
Animals↗
Canadian collaborative project on genetic susceptibility to MS, phase 2: rationale and method. Canadian Collaborative Study Group.
BACKGROUND: Results from the Canadian Collaborative Project on Genetic Susceptibility to Multiple Sclerosis (MS)-Phase 1 (CCPGSMS-Phase 1) together with other family data published since 1982 have led to the following conclusions about the etiology of MS: (i) genetic and non-genetic (environmental) factors are involved in the etiology of MS on a population basis; (ii) the familial aggregation of MS is genetic; (iii) maternal factors do not influence the risk for siblings to develop MS; and (iv) MS appears to be oligogenic. The present paper describes the rationale and methodology for the CCPGSMS-Phase 2. METHOD: The CCPGSMS-Phase 2 is a nation-wide collaborative effort involving all the 15 Canadian MS clinics. A series of structured questionnaires is administered to MS index cases, spouse controls and mothers of index cases and spouse controls (if available) by trained interviewers. Blood samples are taken for molecular genetic studies. This national effort is coordinated by the MS Clinics in Vancouver and London. RESULTS: The CCPGSMS-Phase 2 is in progress so specific results are not available. The study is designed to (i) increase the database for genetic epidemiological/molecular genetic research and (ii) gather population-based data to further our understanding of the non-genetic factors in the etiology of MS. CONCLUSIONS: It is anticipated that the results from this study will impact on the eventual prevention, cure and treatment of MS.
Canada↗
Genetic polymorphisms of histamine degrading enzymes: from small-scale screening to high-throughput routine testing.
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Amine Oxidase (Copper-Containing)↗
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.
BACKGROUND: The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. RESULTS: We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID (http://www.thebiogrid.org) and SGD (http://www.yeastgenome.org/) databases. CONCLUSION: Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks.
Computational Biology↗
Reverse genetic approaches for functional genomics of rice.
T-DNA and transposable elements e.g., Ds and Tos17, are used to generate a large number of insertional mutant lines in rice. Some carry the GUS or GFP reporter for gene trap or enhancer trap. These reporter systems are valuable for identifying tissue- or organ-preferential genes. Activation tagging lines have also been generated for screening mutants and isolating mutagenized genes. To utilize these resources more efficiently, tagged lines have been produced for reverse genetic approaches. DNA pools of the T-DNA tagged lines and Tos17 lines have been prepared for PCR screening of insertional mutants in a given gene. Tag end sequences (TES) of the inserts have also been produced. TES databases are beneficial for analyzing the function of a large number of rice genes.
Binding Sites↗
Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes.
Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes.
Databases, Genetic↗
A comparison of discrete versus continuous environment in a variance components-based linkage analysis of the COGA data.
BACKGROUND: The information content of a continuous variable exceeds that of its categorical counterpart. The parameterization of a model may diminish the benefit of using a continuous variable. We explored the use of continuous versus discrete environment in variance components based analyses examining gene x environment interaction in the electrophysiological phenotypes from the Collaborative Study on the Genetics of Alcoholism. RESULTS: The parameterization using the continuous environment produced a greater number of significant gene x environment interactions and lower AICs (Akaike's information criterion). In these cases, the genetic variance increased with increasing cigarette pack-years, the continuous environment of interest. This did not, however, result in enhanced LOD scores when linkage analyses incorporated the gene x continuous environment interaction. CONCLUSION: Alternative parameterizations may better represent the functional relationship between the continuous environment and the genetic variance.
Alcoholism↗