caTissue: Streamlining Biospecimen Management
One of the cornerstones of effective and efficient biomedical research is having the ability to run experiments and other assays using biospecimens. Researchers who have easy access to relevant tools, biospecimens, and patient information can focus their work on finding cures for cancer and other diseases instead of being bogged down by the logistics of finding appropriate numbers and types of research specimens.
Unfortunately, many researchers may be limited by an inadequate availability of biospecimens relevant to their research and the arduous process of collecting enough samples outside of their own lab. A new caBIG™ software tool called caTissue (developed by the Biomedical Informatics Facility at Washington University in St. Louis, MO) promises to greatly improve the way that biospecimens are catalogued, managed, and accessed—making it easier for researchers across the country to obtain a statistically significant number of specimens for use in experiments.
Why caTissue is important
Traditionally, a researcher, or group of researchers at a specific institution, maintains their own dedicated biospecimen banks, using them for their projects as needed. But the challenge for researchers is that biospecimen repositories maintained by their institutions or partners may not encompass sufficient numbers of the appropriate high quality, clinically annotated biospecimens to achieve the most expeditious and rigorous results.
To facilitate the sharing of specimens among researchers nationwide, the Tissue Banks and Pathology Workspace of caBIG™ has spearheaded an effort to provide the open access caTissue tool to manage a centralized repository describing the location and types of biospecimens across multiple institutions. The Biomedical Informatics Facility at Washington University in St. Louis led the development of this software and was instrumental in assuring its utility for researchers.
How it works
caTissue Core uses a Web-based interface to manage the processing of specimens that are labeled through barcoding systems. This tool helps tissue banks track how tissues have been handled, where they are stored, and how they can be retrieved. A companion application, the cancer Text Information Extraction System (caTIES), enables valuable annotation of specimens by extracting text from pathology and surgical reports, while de-identifying the data to protect patient privacy. An “annotation engine” is also available to retrieve data from additional sources, including medical records, drug treatments, radiology, and tumor registries. Security of patient information and data is carefully controlled through password protection. In addition, only information appropriate to the level of involvement of a user is released.
Both caTissue Core and caTIES are currently available as stand-alone applications and are in use at several institutions. Together, caTissue Core, caTIES, and the annotation engine constitute caTissue Suite, which is due for release in March 2008. Following the adoption and incorporation of caTissue Suite into the local infrastructure of biorepositories at individual institutions, these data resources will be linked to caGrid, the underlying computer architecture that allows data sharing between participating institutions. Researchers will then be able to easily and efficiently query all of the biospecimens stored at their site as well as at other locations around the country.
“Ultimately, caTissue Suite will significantly increase the ability to share databases of available specimens,” said Dr. Ian Fore, Associate Director of Biorepository and Pathology Informatics at NCI. “The seamless sharing of data will be greatly facilitated through caGrid.”
Michael D. Feldman, M.D., Ph.D., Director of the Tumor Tissue and Biospecimen Bank at the University of Pennsylvania anticipates that “the tool, when refined, will enhance the ability of pathologists, biospecimen bankers and other researchers to locate and acquire specimens with the long term goal of catalyzing translational research and optimizing biospecimen banking efforts.”
Adopters like Jack London, Director of the Informatics Core at Thomas Jefferson University’s Kimmel Cancer Center are “looking forward to the release of caTissue Suite when all of these functions can be integrated together,” but he emphasizes that the established protocols for tissue sharing, procurement, fees, or collaboration that are currently in place must still be followed, even with the greater ease of sample discovery and acquisition offered by caTissue Suite to locate specimens of research interest through caGrid.
caTissue in Action
caTissue Core has been adopted by nine institutions around the country who use the tool in several different ways (see list of adopters). For example, institutions have used caTissue Core to:
- Build a Biorepository Core Service Center using caTissue as the foundation software
- Facilitate easier searches for annotated specimens both within and outside the university
- Create a university-wide biospecimen repository focused on cataloguing a wide range of specimen types for clinical research
Status of existing initiatives using caTissue Core:
- The University of Pennsylvania’s Tumor Tissue and Biospecimen Bank is using caTissue Core 1.2 to support its daily biobanking operations with the aim of centralizing and harmonizing all biospecimen banking across the university.
- Thomas Jefferson University’s Kimmel Cancer Center has already extracted annotation data on over 100,000 specimens with caTIES, and researchers are using this tool with caTissue Core to identify biospecimens of interest.
- The Indiana University School of Medicine’s Biorepository has been using caTissue Core for high-throughput biospecimen banking in the departments of pediatrics and ophthalmology since the version 1.2 release in June 2007.
Learn more:
Learn more about NCI's leadership role in guiding biospecimen-related policies and practices:
Office of Biorepositories and Biospecimen Research (OBBR).
