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Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits.
Pubmed ID: 17206864
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Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.
View all literature mentionsThe NTP is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The program maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, the NTP is continually evolving to remain at the cutting edge of scientific research and to develop and apply new technologies. More than 80,000 chemicals are registered for use in the United States. Each year, an estimated 2,000 new ones are introduced for use in such everyday items as foods, personal care products, prescription drugs, household cleaners, and lawn care products. We do not know the effects of many of these chemicals on our health, yet we may be exposed to them while manufacturing, distributing, using, and disposing of them or when they become pollutants in our air, water, or soil. Relatively few chemicals are thought to pose a significant risk to human health. However, safeguarding public health depends on identifying both what the effects of these chemicals are and at what levels of exposure they may become hazardous to humansthat is, understanding their toxicology. The program was created as a cooperative effort to: 1. Coordinate toxicology testing programs within the federal government. 2. Strengthen the science base in toxicology. 3. Develop and validate improved testing methods. 4. Provide information about potentially toxic chemicals to health, regulatory, and research agencies, scientific and medical communities, and the public. The need for a program like the NTP arose because of increasing scientific, regulatory, and Congressional concerns about the human health effects of chemical agents in our environment. Many human diseases were thought to be directly or indirectly related to chemical exposures; therefore, it was thought that decreasing or eliminating human exposures to those chemicals would help prevent some human disease and disability. Testing Information The NTP is an interagency program whose mission is to evaluate agents of public health concern by developing and applying the tools of modern toxicology and molecular biology. This involves conducting toxicological evaluations of substances of public health concern, developing and validating improved (sensitive, specific, rapid) testing methods, developing approaches and generating data to strengthen the science base for risk assessment, and communicating with all stakeholders. The NTP plays a critical role in providing needed scientific data, interpretations, and guidance concerning the appropriate uses of data to regulatory agencies and other groups involved with health-related research. Through its interactive relationship with regulatory agencies, the NTP plays an indirect, but important role in shaping public health policy. Study Data Searches The National Toxicology Program makes available data from more than 500 two-year, two species, toxicology and carcinogenesis studies collected by the NTP and its predecessor, the National Cancer Institute's Carcinogenesis Testing Program, are stored in a database at NIEHS. The NTP database also contains the results collected on approximately 300 toxicity studies from shorter duration tests and from genetic toxicity studies, which includes both in vitro and in vivo tests. In addition, test data from the immunotoxicity, developmental toxicity and reproductive toxicity studies are continually being added to this database. Partnerships Through relationships with regulatory agencies, the NTP has an indirect role in shaping public health policy. Federal and state government agencies rely on the scientific knowledge and its interpretation provided by the NTP to make credible decisions that protect public health and the environment. The NTP also plays a critical role in: 1. Fostering interagency collaborations in research and exposure assessment 2. Providing information to regulatory agencies about alternative methods for toxicity testing, interpretation 3. Exploring new technologies for evaluating how environmental agents cause disease NTP conferences and workshops provide an opportunity for researchers, regulatory, policy makers, and the public to examine issues together, exchange information, and reach agreement on future directions of toxicology and risk assessment. Postdoctoral Training Program Opportunities Applied Toxicology and Carcinogenesis Training Program Fellowship in Toxicological Pathology Fellowship in Laboratory Animal Medicine
View all literature mentionsPortal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.
View all literature mentionsCollection of curated structural variation in the human genome. Catalogue of human genomic structural variation identified in healthy control samples for studies aiming to correlate genomic variation with phenotypic data. It is continuously updated with new data from peer reviewed research studies. The Database is no longer accepting direct submission of data as they are currently part of a collaboration with two new archival CNV databases at EBI and NCBI, called DGVa and dbVAR, respectively. One of the changes to DGV as part of this collaborative effort is that they will no longer be accepting direct submissions, but rather obtain the datasets from DGVa (short for DGV archive). This will ensure that the three databases are synchronized, and will allow for an official accessioning of variants.
View all literature mentionsFunctional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
View all literature mentionsA commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.
View all literature mentionsRoche NimbleGen, Inc. is a leading innovator, manufacturer and supplier of a proprietary suite of DNA microarrays, consumables, instruments and services. Roche NimbleGen uniquely produces high-density arrays of long oligo probes that provide greater information content and higher data quality necessary for studying the full diversity of genomic and epigenomic variation. Roche NimbleGen is enabling a new era of High-Definition Genomics by providing scientists with cost-effective, high-throughput tools for extracting and integrating complex data on important forms of genomic and epigenomic variation not previously accessible on a genome-wide scale. Scientists can thus obtain a clearer understanding of genomic and epigenomic structure and function and how they impact biology and medicine. This improved performance is made possible by Roche NimbleGen''s proprietary Maskless Array Synthesis (MAS) technology, which uses digital light processing and rapid, high-yield photochemistry to synthesize long oligo, high-density DNA microarrays with extreme flexibility. NimbleGen Systems was established in 1999. The MAS technology is the result of research collaborations between the departments of biotechnology, genetics, physics, and semiconductor engineering at the University of Wisconsin - Madison. Roche NimbleGen has the exclusive worldwide license to the MAS technology from the Wisconsin Alumni Research Foundation (WARF).
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
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