Director, James Potter, M.S.
Associate Director, Mimi Canto, M.D.
Tissue Bank Manager, Tyrus Vong
The overarching goal of the Translational Research Enhancement Core (TREC) is to provide the expertise and infrastructure for cost-effective tissue and clinical data collection that meets Best Practices through the establishment of uniform Standard Operating Procedures (SOPs) to promote scientific advances by, and scientific interactions among Core users, collaborative investigators and young investigators. The TREC enhances the value of the biospecimens by their annotation with both clinical and research data.
The TREC was established with the understanding that the uniform and standardized harvest of biospecimens with associated, comprehensive clinical, epidemiological and research data will greatly facilitate and improve the study of gastrointestinal and hepatic disease processes. The TREC consists of a Clinical Research Unit (TREC-CRU) and a Tissue Bank (TREC-TxB). The roles of the TREC-CRU are patient identification, patient recruitment, facilitation of patient trials, translational research and basic research through the creation of a patient registry and database. The TREC director meets with investigators prior to the start of their studies The roles of the TREC-TxB are: to establish Best Practices (BP) and uniform Standard Operating Procedures (SOPs) for specimen collection and management, to support the collection, annotation, processing, storage, management, distribution, and ethical use of human specimens, and to provide access to specimens by investigators.
TREC-TxB (Tissue Bank) Oversight Board. Governance of the TREC-TxB is provided by an oversight board. The Board consists of the DDBTRCC PI (Donowitz), the Core Director (Potter), Co-Director (Brant), one PI from each of the 8 GI areas of research, and at least two rotating independent non-GI JHU investigators. The PI has primary ownership over all tissues directly related to his/her active study project. Guidelines for tissue ownership are given to each PI at the time they begin protocol review and tissue collection. Access to specimens owned by the TREC-TxB (donated by PIs to the TREC-TxB) is granted based on criteria such as scientific merit and clinical significance as determined by the Governance and Oversight Board. Access decisions are guided by a set of general principles defined in the NCI and ISBER Best Practices.
- Barcode Printers/Scanners – Zebra ZM 400 barcode printer and GX430T portable printers for 1D and 2D barcode labels. There are also barcode printers available to study PIs for a small one time fee.
- Laptop and iPad – These portable devices are available and used when accessing specimens in the biorepository facility. They are encrypted and can access the OpenSpecimen server. They also interface with the GX430T portable printer via Bluetooth for barcode label printing.
- Portable Dewar N2 Freezers – Two 4 liter and two 1 liter Dewar freezers are available for the transfer of specimens to the tissue repository.
- Forma Cryo N2 Vapor (LN2) Freezers (-196˚C, 38,500 2 ml vial capacity) – for long term storage. This LN2 freezer is essential for the storage of immortalized cells such as peripheral blood monocytes (PBMC) and for enteroid cell cultures. VWR SYM ULT 25CUFT 220V Mechanical Ultra Low.
- 80˚C Freezers – storage capacity of 40,000 2 ml vials per freezer for short and long-term storage.
- -20˚C Freezer – The -20˚C freezer is used for the short term storage of specimens. These specimens include, but are not exclusive to blood products, urine, and stool.
- 4˚C Refrigerator – The refrigerator is used for the short term storage of some specimens when appropriate and for storage of reagents used in the TREC-TxB.
- Cloud-based Alarm Systems for all freezers – Technicians are automatically contacted by phone, text, and email should a freezer fail (warm). The alarm system includes an O2 sensor due to the use of LN2.
- Centrifuges – Refrigerated centrifuges for blood processing and reagent preparation are available in the adjacent GI Division Equipment Facility on Ross 9. The centrifuges available include two Sorvall Legend RT desktop centrifuges, two Sorvall High-Speed centrifuges, two Beckman Ultra centrifuges, and a small Beckman benchtop ultra.
- Eppendorf 5702 R Portable Refrigerated Centrifuge and Cart – for offsite specimen processing.
- Dry Ice, liquid nitrogen and Thermo Safe Shipping Boxes – for specimen transport and shipping.
- Laminar flow hood – certified for Biosafety Level 1 processing of human specimens.
- Fume hood and flammable storage cabinet – for the storage and handling of flammable reagents.
- Computer System with software including RAID, a data storage technology that provides for data redundancy to protect against disk drive failure, and tape backup. The data is also automatically stored on DOM network servers. These systems are for the monitoring of freezers and the protection of Core D data. The OpenSpecimen application is housed on a server in the SOM Data Facility with security, data backup, and disaster recovery support.
Informatics Solutions and Training
With the rapid data-intensive growth of genomics, proteomics, metabolomics, etc, much of medical and biological research is now data-driven, necessitating informatics solutions for research. Informatics solutions are essential for the annotation of research and clinical data to the biospecimen, and for consent and specimen management. The TREC works in concert with the CTSA and the SOM to develop and enhance these solutions.
Informatics research support tools are provided to the TREC by the CTSA and the SOM. The TREC provides training and assistance with informatics tools necessary to promote clinical and translational research, as well as for biospecimen management. A brief summary and explanation of the informatics tools available to TREC (Core D) Investigators are below. The TREC trains all investigators in the use of these tools.
- OpenSpecimen database – This Biospecimen Information Management System (BIMS) is an Open Source product developed by Krishagni based on the original NCI caTissue and has been adapted for use in a medical department for the management of specimens. The strong user group community furthers the development of OpenSpecimen, which now has improved functionality and ease of use over the earlier NCI product. The OpenSpecimen database is used for specimen inventory management, tracking, and annotation. Investigators can monitor their own collections remotely, but not the collections of other investigators. OpenSpecimen interfaces with EPIC to allow surgical/pathology data to be annotated to specimens inventoried in OpenSpecimen.
- The Clinical Research Management System (CRMS) – CRMS is a translational and clinical research web-based tool meant to streamline study management. It improves communication among study team members, stores subject enrollment information and can run real-time reports. CRMS includes modules for eIRB Submission, Patient Screening, Patient Billing, Patient Calendar/Scheduling, Forms/Clinical Data, Consent Management, and Data Security.
- REDCap – REDCap is a web-based data management tool specifically designed to support data capture for research studies. REDCap allows users to build and manage online databases and surveys quickly and easily and secures and protects PHI. Projects may be built by using the Online Designer, or by creating a data dictionary in Microsoft Excel and then uploading it into REDCap. REDCap sets user privileges and data may be easily exported from REDCap for analysis. The Data Export Tool has advanced features that allow the de-identification of clinical data. An online course is provided by Vanderbilt University, the host of REDCap. REDCap is provided free to the TREC by the SOM.
NEW FOR 2019
TriNetX – To support investigator-led trials
TriNetX is the global health research network enabling healthcare organizations, biopharma and contract research organizations to collaborate, enhance trial design, accelerate recruitment and bring new therapies to market faster. The data in TriNetX is sourced and aligned using Hopkins i2b2 and data in the Hopkins Epic Data Warehouse.
TriNetX is a user-friendly application that enables research collaborations and investigator-led trials through the discovery of de-identified patients (cohorts) that meet a trial’s inclusion/exclusion criteria. Access to further data that contains PHI requires IRB approval and a request to the CCDA (Center for Clinical Data Analytics), which serves as the data honest broker for access to PHI.
PMAP – The Precision Medicine Analytics Platform
Precision Medicine Analytics Platform (PMAP) goes live May 30, 2019
- Hoped to “promote research that will revolutionize the capacity of health centers to continuously improve their patient and population health outcomes at more affordable costs through modern data science and rigorous systems engineering practices.”
- Provides secure access to clinical data, including very different data types: EMR, medical imaging, genomics, biospecimens, and physiological monitoring data. Fields from OpenSpecimen are sent to PMAP to allow for biospecimen discovery with associated clinical data.
- Provides an environment that is built for machine learning and data science to enable discovery
- Detailed advice and assistance with all aspects of specimen collection.
The TREC assists investigators, especially young investigators, with all aspects of clinical trial design and specimen collection, including the planning, cohort discovery, Institutional Review Board (IRB) approval process, the establishment of SOPs for specimen collection, and data collection through training in the use of TriNetX, CRMS, and REDCap.
The TREC assumes the responsibility for the collection, storage, quality assurance, and distribution of specimens as well as the derivation and aliquot dissemination of new specimens from existing ones while following established BPs and SOPs. The TREC technician is responsible for the proper handling of specimens, registry data entry, the cataloging, and storage of specimens and assures the implementation of policies, BPs, and SOPs as established by the Oversight Board and the Director. Both digital and printed manuals of BPs and SOPs are available to investigators.
- Specimen Collection and Management
- The TREC technician works closely with PI directed Nurses, study coordinators and technicians to ensure that all laboratories follow unified SOPs for all tissues to be cataloged and stored in the TREC-TxB. The TREC-TxB technician is responsible for the proper handling of specimens and data entry into the OpenSpecimen DB, catalogs and stores specimens, and is responsible for registry oversight. The TREC-TxB technician has direct access to the cataloged, stored specimens, with back up provided by the Core Director. When possible, the TREC will assist with specimen processing. Studies that necessitate the full assistance of the technician receive first priority. This is determined when studies are initially planned. When necessary, the Core Director assists.
- Nurse or study coordinators working for PIs are responsible for the advanced search and requests for specimen donation, for patient consent, and for data entry into the CRMS patient registry. They are trained jointly by the TREC personnel and by the management team of CRMS.
- Requests for specimens by the PIs or their authorized personnel are processed twice daily. Shipment of specimens to collaborators offsite is performed bi-weekly though more frequently if needed. Transport specifications and tracking of shipments following Best Practices is the responsibility of the TREC and is performed once the PI has obtained an approved MTA (Materials Transfer Agreement). A DUA (Data Use Agreement) is also required if any identifiable PHI (Patient Health Information) is to accompany the specimens.
- Specimen Processing
The TREC-TxB performs routine processing of blood for serum, plasma, and DNA, and collects fresh and cryo-preserved specimens, stool, urine, and sputum. The culture of lymphoblastoid cell lines (PBMCs), as well as the isolation of DNA, RNA, and microRNA from specimens, is also offered.
- Specimen Annotation
Both pre-clinical and clinical data enhance the value of specimens for research and for future collaborations. The options of either direct annotation and/or annotation through informatics solutions are provided to all PIs for their specimen collections.
- Service Request Process
1. The Core director meets with each Investigator to review their protocol, to discuss potential approaches and to provide suggestions and assistance.
2. The Core director provides the guidelines for tissue ownership to each PI at the time they begin protocol review and tissue collection. The document includes a description of the Oversight and Governance board.
3. If training is required, a second meeting is scheduled with either the TREC-TXB technician or the Core director.
4. If priority assistance of the TREC is required, a schedule for that assistance is determined.
5. Follow-up meetings are scheduled to evaluate progress as necessitated by the research protocol.
A table of Charge Back Fees is available on request. Email firstname.lastname@example.org.