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Day Three: Wednesday, May 5

7:30-8:15 Technology Workshop (sponsorship available)

Cancer Biomarker Discovery
 

8:30-8:35 Chairperson's Opening Remarks

Dr. Sudhir Srivastava, Chief, Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute

8:35-9:05 Cancer Detection and Diagnosis: Too Many Biomarkers, Few Validated Tests

Dr. Sudhir Srivastava

Despite our phenomenal success in understanding the biology of tumor and recent advances in genomics- and proteomics-enabled biomarker discovery, only a few tests have been conducted in clinical applications. The lack of research infrastructures and collaborative platforms, in part, has contributed to marginal success in the development of biomarker-based assays for cancer detection and diagnosis. The talk will describe the NCI's Early Detection Research Network and share experience in partnering with academia, industry and clinical institutions on biomarkers discovery, development and delivery.

9:05-9:35  Use of the Serum Fragmentome for Clinical Diagnostics

Dr. Emanuel F. Petricoin, Co-Director, NCI-FDA Clinical Proteomics Program, Senior Principal Investigator, Center for Biologics Evaluation and Research, U. S. Food and Drug Administration

Proteomic patterns of biomarkers from the low molecular weight component of the serum are being successfully used for cancer detection. Mass Spectrometry can generate portrayals of these low molecular weight entities with unmatched speed. Clinical diagnostic applications will require reproducibility performance and new platform development. We are taking advantage of the new discovery that this fragmentome is binding to carrier proteins which serve to amplify, integrate and enrich this information. Nanoharvesting agents are being designed to act as molecular mops for these biomarkers and can be directly queried by mass spectrometry.

9:35-10:05 New DNA Biomarkers for Cancer Diagnosis

Dr. Victor Levenson, Director and Research Associate Professor, Cancer Center, Northwestern University

We developed and tested a new method for high-throughput DNA methylation assay in a defined set of cancer-related genes. When the method was used with an open set of tumors, normal tissues, and morphologically normal tissues adjacent to tumors, we found a specific group of genes that could unambiguously identify each sample. Our method can be used to find similar biomarkers for different tumors and to analyze heterogeneous clinical samples without prior processing; the diagnostic group of genes for analysis can easily be increased, reduced, or otherwise modified for a specific application.

10:05-10:45 Coffee Break with Poster and Exhibit Viewing

 

10:45-11:30 Working with Human Tissues for Biomarker Discovery and Validation

Chairperson: Dr. Kevin Krenitsky, Sr. Vice President, Medical Director, Genomics Collaborative, Inc.   PANELISTS: • Dr. Mike Severino, Director of Molecular Profiling, Merck • Dr. Sudhir Srivastava, Chief, Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute • Additional Panelists to be Announced   DISCUSSION TOPICS: • What are some "best practices" to follow in sourcing human tissue? • What tissue format (Snap frozen, FFPE blocks, etc.) provides the best opportunity for Biomarker discovery? • What are the major bottlenecks in obtaining human cancer tissue for research? • What are the main ethical concerns in sourcing and using human tissue? • What are some emerging technologies that are becoming valuable in human tissue research? • What are the preferred phenotypic parameters needed to accompany the actual tissue sample? • How does tissue research relate to biomarker discovery and/or validation in the diagnostic and therapeutic arenas?

11:30-12:15 Keynote Address: Personalizing Cancer Medicine

Prof. Karol Sikora, Scientific Director, Oncology, Medical Solutions

The biomarkers and surrogates used in drug development will also be adapted by the end of the decade to individualize therapeutic programs. This will revolutionize the delivery of cancer care from an organocentric to a genocentric model. This will have profound funding consequences and require a major investment in sophisticated diagnostic tools.

12:15-1:45 Lunch (on your own) or Technology Workshop (sponsorship available)

Validation of Cancer Biomarkers

1:45-1:50 Chairperson's Opening Remarks

Prof. Karol Sikora, Scientific Director, Oncology, Medical Solutions

1:50-2:20 Validating New Biomarkers in the Diagnosis and Management of Cancer

Professor Christopher P. Price, Vice President, Clinical Research, Diagnostics Division, Bayer Healthcare

Detection and measurement of biomarkers in the bloodstream provides the most practical means for screening, diagnosis and management of malignant disease; these include protein, peptide and nucleic acid moieties. As more drugs target specific pathophysiological changes, new complementary proteomic and genomic markers will be discovered which will need to be validated in parallel with the therapeutic intervention. Validation of new markers should focus on the impact of measurement for improving clinical decision-making and on health outcomes.

2:20-2:50 Genomic Strategies for Discovery and Validation of Biological Markers for Cancer Diagnosis: From Gene Expression to Human Serum

Dr. Jackie Papkoff, Vice President, Target Discovery and Validation, Discovery, diaDexus, Inc.

We have utilized a comprehensive data mining approach coupled with subtractive library evaluation to identify candidate genes for our biomarker program in cancer. Sequences are curated and prioritized using a variety of molecular and bioinformatics tools, including custom oligonucleotide arrays, quantitative PCR with panels of tumor and normal tissues, and a proprietary in-house database of predicted splice variants. We focus on secreted, up-regulated leads where we produce recombinant monoclonal antibodies and evaluate protein expression by ELISA in disease-relevant human serum samples. Highlights of the discovery and validation tools and process will be presented along with selected examples of our diagnostic leads.

2:50-3:20 Statistical Considerations for Biomarker Clinical Validation

Dr. Ziding Feng, Professor, Public Health Science, Fred Hutchinson Cancer Research Center

We will discuss guidelines for biomarker clinical validation in the context of cancer early detection. Statistical considerations include the design of validation studies, data analysis and interpretations, and how to move the biomarkers through the pipeline towards clinical validation in a rigorous manner. Examples are drawn from the studies conducted in Early Detection Research Network (EDRN).

3:20-4:00 Refreshment Break with Poster and Exhibit Viewing

4:00-4:30 Identification and Validation of Serum Biomarkers for Colorectal Cancer

Dr. Chris Burgess, Principal Staff Scientist, Genomics and Bioinformatics, Bayer Diagnostics

Identification and validation of serum biomarkers for colorectal cancer disease-specific biomarkers will have a profound impact on patient management, by enabling early detection of disease, detecting disease recurrence, and monitoring for therapeutic efficacy. Given the complex nature of most diseases, including cancer, it is unlikely a single predictive biomarker will satisfy the requisite performance criteria; instead, a panel of markers needs to be configured. We will present recent findings on our collaborative effort with investigators at the Mayo Clinic to identify, validate, and commercialize a panel of protein biomarkers for management of colorectal cancer.

4:30-5:00 Validation of Biomarkers for Cancer Diagnostics

Dr. Abhijit "Ron" Mazumder, Manager, Technology Development, Molecular Diagnostics, Veridex, LLC, a Johnson & Johnson Company

High-density DNA microarrays are a powerful tool for the discovery of novel markers that can be used in the detection, staging, and prognosis of tumors; however, development of diagnostic assays in a PCR-based format often requires validation of these markers. Workflows and lessons learned during this process will be presented.

5:00 Close of Cancer Biomarkers meeting

 

Ciphergen Seminar

Biomarker Discovery, Validation, Identification and Assay Development Thursday, May 6th, 2004 • Park Hyatt, Philadelphia, Pennsylvania A free seminar to hear about Ciphergen's ProteinChip Systems for the study of biomarkers and functional proteomics, along with real-world application stories by prominent users of SELDI (Surface-Enhanced Laser Desorption/Ionization) technology.   More info: visit http://www.ciphergen.com/about_us/events/local/cbiEventInfo.asp?id=20   To register, please check off the appropriate box on the registration page.   Ciphergen develops, manufactures and markets ProteinChip® Systems that enable protein discovery, characterization and assay development so that researchers can gain a better understanding of biological functions at the protein level. ProteinChip Systems are powerful tools that provide a direct approach to understanding the role of proteins in the biology of disease, monitoring of disease progression and the therapeutic effects of drugs. Pioneering researchers around the world are taking full advantage of Ciphergen's powerful SELDI-based ProteinChip platform to advance clinical and research proteomics for biomarker and target discovery. Learn more at www.ciphergen.com.