A novel cross-disciplinary multi-institute approach to translational cancer research: Lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)

Ashokkumar A. Patel, John R. Gilbertson, Louise C. Showe, Jack W. London, Eric Ross, Michael F. Ochs, Joseph Carver, Andrea Lazarus, Anil V. Parwani, Rajiv Dhir, J. Robert Beck, Michael Liebman, Fernando U. Garcia, Jeff Prichard, Myra Wilkerson, Ronald B. Herberman, Michael J. Becich, Nancy Whelan, Lois Mathews, Sharon WintersSusan Urda, Heidi Gianella, Michelle Bisceglia, Rajnish Gupta, Harpreet Singh, Songhui Li, Yimin Nie, Vicky Chu, Sambit Mohanty, Dorothy Mann, Linda Mignogna, Federico Monzon-Bordonaba, Alice Katsur, John Kirkwood, Adam Brufsky, Theresa Colecchia, Carolyn Green, John Glick, Jesse Tigges, David Fenstermacher, Timothy R. Rebbeck, Angela DeMichele, Barbara Weber, Du Pont Guerry, Elizabeth Poppert, Kate Haney, Steve Brusstar, John Malick, Arlene Capriotti, Andrew Balshem, Robert G. Uzzo, Lori J. Goldstein, Stuart R. Lessin, Pat Harsche, W. Thomas London, Richard L. Davidson, Monica DeBaca, Alejandra Ruiz Orrico, Adler Hannes, Juan P. Palazzo, Adam Dicker, Michael Mastrangelo, Katherine Chou, Thomas Loughran, Pam Whayland, Pat Swetland, Philip Lazarus, Isom Harriet, Dan Beard, Alan J. Snyder, Witold B. Rybka, Daniel Lorence, Allan Lipton, Harold A. Harvey, Gavin Robertson, David Claxton, Richard Rauscher, Jenine Carlisle, Russel E. Kaufman, Donald Ewert, Elizabeth O'Brien, Meryle Melnicoff, Kenneth Blank, Tesfu Hailu, Sokol Petushi, Glenn D. Steele, Sandy Buckley, Nicole Hunter, Kim Yantus, Hai Hu, Chris Sheridan, Holly Rigby, F. Nicholas Jacobs, Pat Bronder, David Palmer, John H. Glick

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Background: The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu) is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1) for bioinformatics and a repository of serum and tissue samples; (2) a data model for biomarker data storage; and (3) a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium's intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancerspecific biomarkers and encourage collaborative research efforts among the participating centers. Methods: The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission. The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual property/tech transfer agreements, and material transfer agreements that have been approved by each of the member institutions. This was the foundational work that has led to the development of a centralized data warehouse that has met each of the institutions' IRB/HIPAA standards. Results: Currently, this "virtual biorepository" has over 58,000 annotated samples from 11,467 cancer patients available for research purposes. The clinical annotation of tissue samples is either done manually over the internet or semiautomated batch modes through mapping of local data elements with PCABC common data elements. The database currently holds information on 7188 cases (associated with 9278 specimens and 46,666 annotated blocks and blood samples) of prostate cancer, 2736 cases (associated with 3796 specimens and 9336 annotated blocks and blood samples) of breast cancer and 1543 cases (including 1334 specimens and 2671 annotated blocks and blood samples) of melanoma. These numbers continue to grow, and plans to integrate new tumor sites are in progress. Furthermore, the group has also developed a central web-based tool that allows investigators to share their translational (genomics/proteomics) experiment data on research evaluating potential biomarkers via a central location on the Consortium's web site. Conclusions: The technological achievements and the statewide informatics infrastructure that have been established by the Consortium will enable robust and efficient studies of biomarkers and their relevance to the clinical course of cancer.

Original languageEnglish
Pages (from-to)255-274
Number of pages20
JournalCancer Informatics
StatePublished - 2007
Externally publishedYes


Dive into the research topics of 'A novel cross-disciplinary multi-institute approach to translational cancer research: Lessons learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)'. Together they form a unique fingerprint.

Cite this