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The NIDDK Central Repository at 8 years--ambition, revision, use and impact.

The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Central Repository makes data and biospecimens from NIDDK-funded research available to the broader scientific community. It thereby facilitates: the testing of new hypotheses without new data or biospecimen collection; pooling data across several studies to increase statistical power; and informative genetic analyses using the Repository's well-curated phenotypic data. This article describes the initial database plan for the Repository and its revision using a simpler model. Among the lessons learned were the trade-offs between the complexity of a database design and the costs in time and money of implementation; the importance of integrating consent documents into the basic design; the crucial need for linkage files that associate biospecimen IDs with the masked subject IDs used in deposited data sets; and the importance of standardized procedures to test the integrity data sets prior to distribution. The Repository is currently tracking 111 ongoing NIDDK-funded studies many of which include genotype data, and it houses over 5 million biospecimens of more than 25 types including serum, plasma, stool, urine, DNA, red blood cells, buffy coat and tissue. Repository resources have supported a range of biochemical, clinical, statistical and genetic research (188 external requests for clinical data and 31 for biospecimens have been approved or are pending). Genetic research has included GWAS, validation studies, development of methods to improve statistical power of GWAS and testing of new statistical methods for genetic research. We anticipate that the future impact of the Repository's resources on biomedical research will be enhanced by (i) cross-listing of Repository biospecimens in additional searchable databases and biobank catalogs; (ii) ongoing deployment of new applications for querying the contents of the Repository; and (iii) increased harmonization of procedures, data collection strategies, questionnaires etc. across both research studies and within the vocabularies used by different repositories.

Pubmed ID: 21959867 RIS Download

Mesh terms: Animals | Biological Specimen Banks | Database Management Systems | Databases, Factual | Diabetes Mellitus | Digestive System Diseases | Humans | Kidney Diseases | National Institute of Diabetes and Digestive and Kidney Diseases (U.S.) | United States

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This is a list of tools and resources that we have found mentioned in this publication.


dbGaP at NCBI

Database to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype, including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. dbGaP provides two types of access for users, open and controlled. Summaries of studies and the contents of measured variables as well as original study document text are generally available to the public, while access to individual-level data including phenotypic data tables and genotypes require varying levels of authorization. The data in dbGaP will be pre-competitive, and will not be protected by intellectual property patents. Investigators who agree to the terms of dbGaP data use may not restrict other investigators' use of primary dbGaP data by filing intellectual property patents on it. However, the use of primary data from dbGaP to develop commercial products and tests to meet public health needs is encouraged. Submitters who are not Federally-funded and affiliated with an NIH IC will need to work with an NIH DAC so that proposed submission can be reviewed for consistency with appropriate policies to protect the privacy of research participants and confidentiality of their data. Submissions to dbGaP will not be accepted without assurance that the submitting institution approves the submission and has verified that the data submission is consistent with all applicable laws and regulations, as well as institutional policies. Submitters must also identify any limits on research uses of the data that are specifically set by individual research participants, e.g., through their informed consent. Open-access data can be browsed online or downloaded from dbGaP without prior permission or authorization.

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NIDDK Central Repository

Data, biosample, and genetic repositories to increase the impact of current and previously funded NIDDK studies, making the data and biospecimens available to the broader scientific community. These Repositories enable scientists not involved in the original study to test new hypotheses without any new data or biospecimen collection, and provide the opportunity to pool data across several studies to increase the power of statistical analyses. In addition, most NIDDK-funded studies are collecting genetic biospecimens and carrying out high-throughput genotyping making it possible for other scientists to use Repository resources to match genotypes to phenotypes and to perform informative genetic analyses. There are three Repositories: * Biosample Repository - Fisher BioServices, Inc (14665 Rothgeb Drive, Rockville, MD 20850) Receives biosamples collected in many different studies, stores the samples under optimal conditions, and distributes them to qualified investigators. * Genetics Repository - Rutgers, The State University of New Jersey (Rutgers Lab)(604 Allison Road, Nelson Labs C112, Piscataway, NJ 08854) Receives blood samples collected in many different studies, and processes them to create immortalized cell lines, and DNA samples. They also cryopreserve blood cells, extract DNA from blood samples, store samples of DNA under optimal conditions, and distribute DNA samples to qualified investigators. * Central Data Repository (CDR) - RTI International (3040 Cornwallis Rd, Research Triangle Park, NC 27709) Receives, archives, maintains and distributes databases or parts of databases from studies. In addition, they analyze stored data in response to inquiries, assist ongoing studies in preparing data for eventual archiving, coordinate cross-referencing between the three Repositories, and maintain the Central Repository website. The NIDDK Central Repositories have four major components: * An archive of clinical data and documentation from NIDDK-sponsored studies * A collection of biospecimens and an associated database that identifies specimens collected from ongoing and completed studies funded by NIDDK and links them to the associated phenotypic data * A web portal that makes study-specific information within the Repository easily viewable and that accepts electronic requests for biospecimens and data * A collection of genotyping data from GWAS and sequencing studies housed at the National Center for Biotechnology Information's (NCBI) database of Genotypes and Phenotypes (dbGaP)

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