Translational Research Enhancement Core

James Potter Director
James Potter, MS
Steven R. Brant Associate Director
Steven R. Brant, MD

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, without each investigator having to invest in the equipment/resources or to individually work out the specific SOPs.
The Translational Research Enhancement Core was established with the understanding that the uniform and standardized harvest of biospecimens with associated, comprehensive clinical and epidemiological data will greatly facilitate and improve the study of gastrointestinal and hepatic disease processes. The Translational Research Enhancement Core (Tissue Repository) 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 creation of a patient registry and database. The director of the TREC 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 the collection, annotation, processing, storage, management, distribution, and ethical use of human specimens, and to provide access to specimens by investigators.

TREC-TxB Oversight Board. Governance of the GI-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 GI-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 a GX430T portable printers for 1D and 2D barcode labels.
  • 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 2 – 1 liter Dewar freezers are available for 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). VWR SYM ULT 25CUFT 220V Mechanical Ultra Low Freezers (-80°C) – 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 GI-TxB. 
  • Alarm Systems for all freezers – Technicians are automatically contacted by phone 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 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 which provides for data redundancy to protect against disk drive failure, and tape backup — for the monitoring of freezers and protection of Core D data. The OpenSpecimen application is housed on a server in the SOM with security, data backup and disaster recovery support.

     — Informatics
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 Core D by the CTSA and the SOM. The TREC provides assistance with informatics necessary to promote clinical and translational research, as well as for specimen management. A brief summary and explanation of the informatics tools available to Core D Investigators is below. Core D trains all investigators in the use of these tools.

  • OpenSpecimen (formerly caTissue Plus 3.0) 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. OpenSpecimen 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. Currently, the SOM is working to interface surgical/pathology data with 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.
  • i2b2 (Informatics for Integrating Biology and the Bedside) - i2b2 is an NIH funded National Center for Biomedical computing at Partners HealthCare System and has been adopted by the Hopkins CTSA. I2b2 enables cohort and specimen discovery from existing clinical data to enhance clinical and translational research. All data is de-identified and the i2b2 tool is a self-help product. 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. I2b2 is currently being developed to interface surgical/pathology data with specimens inventoried in OpenSpecimen.
  • EPIC for Clinical Research (Cogita Data Warehouse). The Director of the TREC, Jim Potter, is an EPIC superuser and helped to hire a team to enable EPIC for translational and clinical research. The School of Medicine is building an EPIC (Cogita) Data Warehouse to facilitate research access to patient data. EPIC EHR data is migrated to the Cogito Data Warehouse nightly where it is then available for research use. The CCDA (Center for Clinical Data Analytics) serves as the data honest broker for access to PHI data.
  • 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 de-identification of clinical data. An online course is provided by Vanderbilt University, the host of REDCap. REDCap is provided free to Core D by the SOM.


  • Detailed advice and assistance with all aspects of specimen collection.

Core D assists investigators, especially young investigators, with all aspects of specimen collection, including the planning, Institutional Review Board (IRB) approval process, the establishment of SOPs for specimen collection, and data collection using CRMS (Clinical Research Management System) as well as REDCap (Research Data Capture).
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 GI-TREC-TxB 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 GI-TREC-TxB. The GI-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. GI-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 Core D 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 Core D 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. Due to demand, the culture of lymphoblastoid cell lines (PBMCs) is now offered, as well as the isolation of DNA, RNA, and microRNA from specimens.

  • Specimen Annotation

Both pre-clinical and clinical data enhances the value of the specimens for research and for future collaborations. The options of either direct annotation and/or annotation through informatics solutions is provided to all PIs for their specimen collections.

  • Service Request Process
  • The Core director meets with each Investigator to review their protocol, to discuss potential approaches and to provide suggestions and assistance.
  • 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.
  • If training is required, a second meeting is scheduled with either the GI-TRC-TXB technician or the Core director.
  • If priority assistance of the core is required, a schedule for that assistance is determined.
  • Follow-up meetings are scheduled to evaluate progress as necessitated by the research protocol.

skype You will need Skype Credit