Genetic Alliance BioBank has the following technical components along with an integrated biorepository.
TRIMS Registry The TRIMS implementation for GABB is an Application Service Provider (ASP) model hosted and maintained by Gene Logic. TRIMS is a centralized data repository for annotation data (clinical and experimental), sample source and handling information, processing and quality assurance (QA) information, as well as inventory and process flow data. All clinical, demographic, and experimental data management and sample registration/accessioning occur in TRIMS. TRIMS also provides tracking, data query, report generation, and process management functions. TRIMS currently supports more than 185,000 records with thousands of standard fields and unlimited customizable fields for the collection of clinical information. TRIMS uses SNOMED, from the College of American Pathologists, as the controlled vocabulary for classification of disease and sample morphology. TRIMS also uses internal standards for controlling the quality and consistency of entered data including use of drop-down pick lists, flexible units translation, and field data type restrictions among others. Further, the system administrator can control and modify many of these attributes for particular fields to tailor the acceptable input values. TRIMS is built on industry-standard architectures based on COTS application platforms. The application software utilizes J2EE architecture, Microsoft Visual Basic, and an Oracle database with a robust baseline database schema that is readily extensible and customizable to accommodate various data and interface requirements. It uses Sun Enterprise™ or Sun Fire™ server hardware for high-reliability and scalability. Online Clinical Questionnaire System GABB TRIMS system provides member organizations the ability to implement customized Web-based questionnaires for the collection and management of participant clinical data. This secure system has administrative and end-user functionality. Member organizations administer the questionnaires and have secure access to the application where they can register questionnaire users, request a user to fill out a questionnaire by sending a request e-mail, and review, approve, or reject completed questionnaires. End-users can be participants, providers, parents, or any other designated third party. Users have secure access to the questionnaire application where they can consent to complete the questionnaire, directly navigate to specific pages or sections, and complete the questionnaire partially or fully. Multiple answer types are supported including free text, drop-down lists and check boxes. Data checks exist for consistency by page and dependency for the entire questionnaire, and data is saved to the database every time the user leaves the page. Users can review the data by section, mandatory questions, unfilled questions or the complete questionnaire before submitting the questionnaire. Action Request System Once a participant has been consented, they are eligible to donate a sample or data to the BioBank. The Action Request System is their first point of entry. The Action Request System is utilized to request that an action be performed by the Gene Logic biorepository personnel, such as sending out sample collection kits to donors or sending biological samples to authorized investigators. The Action Request System provides Web-based, secure access to the application for participant registration and is administered by the member organization´s designated representative. The participant´s name, contact information, and the type of kit requested (if a sample will be collected) are entered. This triggers Gene Logic to accession the participant into TRIMS and send the kit, with customized instructions for sample collection, to the participant. Once the sample donation is complete (in most cases a blood draw by a phlebotomist, nurse or physician), the kit is returned to Gene Logic by a prepaid Fed Ex mailer. Each kit comes with all necessary components and instructions. Arrangements can be made to ship multiple kits (e.g. for patient outreach events). Kit shipment and receipt can be tracked within the Action Request System. The Action Request System also has secure activity logging and provides summary reporting for all distribution activities (collection kits and samples) as well as for billable events, inventories and accounting. Data Mining Capabilities The Genesis Enterprise System Software data mining software provides GABB members with extensive search capabilities tailored to the clinical and experimental data stored in the TRIMS warehouse. It provides access to the sample annotations for clinical, medical, family history, and experimental information that accompanies each donor and sample registered in TRIMS. The Genesis Sample Query Tool is used to select criteria, query the clinical database and select cohorts or sets of samples with specific characteristics using any of the hundreds of clinical and experimental attributes contained in the database. Genesis provides a collaborative, secure environment that incorporates integrated visualization tools that allow users to examine clinical data and sample attributes simultaneously and perform a wide variety of analyses. The system enables the easy creation and management of a large number of sample sets and storage and sharing of the analysis results for ongoing investigations. Genesis has secure, administrator-controlled access permissions and automated workflow templates for managing end-user access and enterprise sharing of analyses and data. This tool allows the researcher to fully customize the layout and presentation of results, findings and analyses in order to aid in the discovery of critical and valuable information. Integrated Centralized Biorepository Gene Logic´s Biorepository is responsible for receiving and accessioning all incoming samples. The Biorepository provides shipping, receiving and handling services for all biological samples. Processes and procedures have been established to ensure compliance with domestic and international regulations and guidelines and to ultimately ensure that all samples are handled in a manner that will preserve the quality of the material both in transit and at Gene Logic. To date, this department has successfully handled more than 185,000 biological samples. The Biorepository has worked with over 150 sites to accrue tissue, RNA and DNA of interest. Sites must have evidence of IRB approval and comply with all relevant confidentiality regulations. Chain of Custody and Audit Tracking Gene Logic provides chain of custody information and audit tracking for all processes described above. The TRIMS system includes a fine-grained hierarchy of authentication with users, groups, permissions and roles. Information in TRIMS has an owner and a permission object with a user´s privileges verified prior to displaying or changing a data point. The Online Clinical Questionnaire System provides authentication, has secure activity logging, and provides summary reports for all distribution activities (collection kits and samples) as well as for billable events, inventories, and accounting. A site administrator creates users and groups and establishes roles and permissions. Authentication logs are maintained to show changes to permissions and access as well as to all data fields. |
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