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Expression Project for Oncology (expO) completes first phase of standardized gene expression analyses

The International Genomics Consortium’s (IGC) Expression Project for Oncology (expO) has released clinically annotated gene expression profiles for 60 tumor specimens, completing the initial phase of the nation’s first and eventually largest public database dedicated to standardized gene expression data. The clinically annotated dataset is available in the public domain through the National Center for Biotechnology Information web site at www.ncbi.nlm.nih.gov/geo/.

The goal of expO and its consortium supporters is to procure tissue samples under standard conditions and perform gene expression analyses on a clinically annotated set of deidentified tumor samples updated with clinical outcomes and release all data into the public domain without intellectual property restriction.

"This publicly accessible gene expression clinical database of patient specimens will fuel and accelerate clinically meaningful and scientifically valid research into better prognostic tests, new diagnostics, targeted therapies, predictive therapeutic strategies and potentially preventative modalities for patients" said IGC’s founder, Daniel Von Hoff, MD, FACP.

IGC has established a uniform system for obtaining and processing tissue samples for molecular characterization studies. Clinical annotation for each tissue sample will enable researchers to form testable clinical hypotheses for use in future treatment decision making. Tissue collection and data dissemination will be conducted in a manner that fully protects patient privacy. Over a three-year period, IGC expects to obtain 2,000 to 3,000 tumor specimens representing a broad spectrum of malignancies and 500-1,000 normal tissues.

expO has exceeded its first-year milestone of collecting consented and clinically annotated tumor biospecimens in a highly standardized format by 65%. This accomplishment puts expO on a projection to exceed its targeted collection and gene expression of 1,900 tumor biosamples over the course of 3 years.

Standardization of the collection, analysis, and vocabularies will help accelerate future development of new, targeted cancer treatments. Standardization, which will take place at every phase from consent to collection to gene expression, will result in better patient care.

Collaboration with the participating medical centers in the mechanics of tumor collection has also improved the quality of the collected tissues. The collection of tumor samples from surgery is historically difficult to achieve rapidly, due to the number of handling and review steps required to insure that the release of that tumor sample in no way jeopardizes patient care. Nonetheless, rapid handling is a necessity in order to maintain the integrity of RNA by quickly freezing the portion of tumor released for analysis. Historically, collection efforts typically achieve a successful preservation rate of 75%. Due to close collaboration between the surgeons, pathologists, local clinical research coordinators and expO, the success rate achieved in preserving these samples was 100%. Such well-preserved tissue allows the subsequent analysis to more precisely reflect the tumor’s biology.

"We are very pleased with the significant successes the project has achieved in our first year,"?said Robert Penny, M.D., Ph.D, Executive Director of expO and Chief Medical Officer of IGC. "These findings will be of benefit to the worldwide research community."

Consortium funding for expO’s launch comes from six international pharmaceutical firms. Major sponsors are Bristol-Myers Squibb, GlaxoSmithKline, Wyeth and IBM. Other sponsors are Pfizer, Aventis,

Johnson & Johnson, Flinn Foundation, ILEX Oncology, and Genomics Collaborative Inc. Research support from Affymetrix, AmeriPath, the Georgia Cancer Coalition, Agilent Technologies, Amersham Biosciences, and Telik Inc. also springboards the effort.

Major founding support was provided to IGC from Ari zona State University, the City of Phoenix, and from Maricopa County in Arizona.


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Source:International Genomics Consortium


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