A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)
Authors: Patel Ashokkumar A. , Gilbertson John R. , Showe Louise C. , London Jack W. , Ross Eric , Ochs Michael F. , Carver Joseph , Lazarus Andrea , Parwani Anil V. , Dhir Rajiv , Beck J. Robert , Liebman Michael , Garcia Fernando U. , Prichard Jeff , Wilkerson Myra , Herberman Ronald B. , Becich Michael J. ,   PCABC, Whelan Nancy , Mathews Lois , Winters Sharon , Urda Susan , Gianella Heidi , Bisceglia Michelle , Gupta Rajnish , Singh Harpreet , Li Songhui , Nie Yimin , Chu Vicky , Mohanty Sambit , Mann Dorothy , Mignogna Linda , Bordonaba Federico Monzon , Katsur Alice , Kirkwood John , Brufsky Adam , Colecchia Theresa , Green Carolyn , Glick John , Tigges Jesse , Fenstermacher David , Rebbeck Timothy R. , DeMichele Angela , Weber Barbara , Guerry DuPont , Poppert Elizabeth , Haney Kate , Brusstar Steve , Malick John , Haney Kate , Capriotti Arlene , Balshem Andrew , Uzzo Robert G. , Goldstein Lori J. , Lessin Stuart R. , Harsche Pat , London W.Thomas , Davidson Richard L. , deBaca Monica , Orrico Alejandra Ruiz , Hannes Adler , Palazzo Juan P. , Dicker Adam , Mastrangelo Michael , Chou Katherine , Loughran Thomas , Whayland Pam , Swetland Pat , Lazarus Philip , Harriet Isom , Beard Dan , Loughran Thomas , Snyder Alan J. , Rybka Witold B. , Lorence Daniel , Lipton Allan , Harvey Harold A. , Robertson Gavin , Claxton David , Rauscher Richard , Carlisle Jenine , Kaufman Russel E. , Ewert Donald , O'Brien Elizabeth , Melnicoff Meryle , Blank Kenneth , Hailu Tesfu , Petushi Sokol , Steele Glenn D. , Buckley Sandy , Hunter Nicole , Yantus Kim , Hu Hai , Sheridan Chris , Rigby Holly , Jacobs F. Nicholas , Bronder Pat , Palmer David , Glick John H. 
Published: October 2017

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 cancer-specific 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 semi-automated 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.