Instructors: John L. Allinson, FIBMS, Director, Veeda Clinical Research Ltd.; and Viswanath Devanarayan, Ph.D., Director, Statistics, Biomarker Research, Abbott Laboratories

This tutorial will focus on the recommendations for the best practices in the development and validation of bio-marker assay development, method validation and sample analysis, with special emphasis on assays where a reference standard material is available. First, an introduction to the concept of “Fit-for-Purpose” method valida-tion, the different types of biomarker methods & data, and a broad roadmap to method development and valida-tion will be provided. The key elements of fundamental validity to meet the objectives of exploratory biomarker studies will be discussed, including the basic requirements such as sample stability and collection integrity, vali-dation and QC samples, calibration curve fitting methods, method optimization and method feasibility studies. The elements of more extensive assay validation (“advanced” validation), needed for the chosen biomarkers in pivotal studies will, then be discussed. Finally, the recommendations for pre-study and in-study validation will be provided with case illustration.

Coverage Includes:

1. Introduction - Nomenclature, types of biomarker methods/assays, biomarker method development & validation road-map, fundamental validity, similarity to PK assays & difference from diagnostic application.. 
2. Pre-analytical and Bioanalytical elements: Target range, standards, validation & QC samples, stability, matrix ef-fect, and relative selectivity.
3. Calibration curve model selection, evaluation, and weighting.
4. Method feasibility and optimization with precision profiles.
5. Evaluation of some pre-study validation characteristics such as precision, bias, sensitivity and quantification limits.
   Illustrations of pre-study validation and in-study validation (sample analysis).

8:00-11:00 Pre-Conference Workshop* 
(*Separate Registration Required)

Sponsored by 

8:00-8:10 Chairperson’s Opening Remarks

8:10-8:40 Evaluation of microRNAs for Diagnosis and Prognosis of Patients with Solid Tumors
Mitch Raponi, Ph.D., Principal Research Scientist, Biomarkers and Translational Research, Centocor Research & Development
microRNAs (miRNA) are short non-coding RNAs that control the expression of multiple proteins through various mechanisms. It has been shown that miRNAs are differentially expressed in different cancers and limited func-tional studies have implicated specific miRNAs as either oncogenes or tumor suppressors. Using various expres-sion profiling technologies (Ambion miRVana BioArray, Agilent miRNA microarray, Applied Biosystems Taqman miRNA assays) we have identified and evaluated miRNAs that are potential diagnostic and prognostic biomarkers for colorectal cancer (CRC) and squamous cell lung cancer, respectively. In addition, functional studies of se-lected miRNAs have provided insight into their biochemical role in CRC. The utility of these analytes compared to previously defined mRNA classifiers will be discussed as well as the performance of different profiling platforms. 

8:40-9:10 Her2/neu, microRNAs and Herceptin
Michael N. Liebman, Ph.D., Senior Institute Fellow, Windber Research Institute
Herceptin treatment in breast cancer requires the observance of overexpression of Her2/neu in the patient, as measured by FISH and/or IHC. Only 25% of all patients overexpress her2/neu, and only 40% of these patients respond to Herceptin. In collaboration with BIOBASE, we have pursued upstream analysis of the observed gene expression differences in patients where FISH and IHC present different results and have determined that a mi-croRNA appears to function as a switch in determining the differential response. This has been analyzed in terms of its potential use as a diagnostic and/or therapeutic target to improve decision-making for treatment in breast cancer patients.

9:10-9:30 The Need for Quantitation in miRNA Biomarker Assays
Sponsored by 
Keld Sorensen, Ph.D., Director, Research & Development, Luminex Bioscience Group
Numerous methods exist for the detection on miRNAs, including qRT-PCR, planar arrays, bead based arrays and others. Synthetic miRNAs are an ideal material for creating standard curves for these assays. This presentation will compare and contrast each type of assay with respect to the use of standards for use in biomarker development. 

9:30-10:00 Networking Coffee Break

10:00-10:30 Discovery of miRNA-Based Biomarkers for Cancer
Søren Møller, Ph.D., CSO, Vice President, R&D, Exiqon A/S 
Abnormal expression of microRNAs (miRNAs) in cancer implies that these small ~22-nucleotide molecules play a role in oncogenesis. Therefore, miRNAs may comprise a novel class of diagnostic and prognostic signatures. This talk will focus on examples of using microRNA for cancer classification, prognosis and treatment selection. 

10:30-11:00 Analysis of microRNAs in Pancreatic Fine Needle Aspirates and Archived FFPE Specimens Can Classify Benign and Malignant Tissues
Anna E. Szafranska, Ph.D., Senior Scientist, Asuragen Inc. 
Patients diagnosed with pancreatic ductal adenocarcinoma (PDAC) typically have a poor prognosis due to its very aggressive local invasion and high metastatic potential coupled with the lack of robust early detection methods and effective treatments. Altered expression of mature microRNAs (miRNAs) has been shown to reliably identify pancre-atic tissue disease status in frozen human clinical specimens (Szafranska et al., Oncogene 2007). Here we report that the expression level of as few as two miRNAs, miR-196a and miR-217, in fine needle aspiration (FNA) biopsies or in archived Formalin-Fixed, Parafin-Embeded (FFPE) tissues can distinguish PDAC specimens from normal pan-creas and chronic pancreatitis specimens. This study indicates that miRNA expression analysis in pancreatic clinical samples can aid pathological evaluation of suspicious cases and may provide a new strategy for improving the di-agnosis of pancreatic diseases.

12:00-3:00 Pre-Conference Workshop* 
(*Separate Registration Required)

12:00-12:30 Circulating Tumor Cell Assays: A Prognostic and Predictive Factor for Breast, Prostate and Colon Cancer
Herbert A. Fritsche, Ph.D., Professor and Chief of Clinical Chemistry, The University of Texas M. D. Anderson Cancer Center
The current hypothesis of cancer metastasis suggests that tumor cells are released into the blood and circulate until they are either eliminated by host response mechanisms or until they find an environment in which to reside and proliferate. Thus, assays for the detection of circulating tumor cells may provide information useful for clini-cal management of cancer. One assay method (Veridex Inc., Cell Search) has been cleared by the FDA for use as a prognostic test in metastatic breast cancer patients, and more recently, for both prostate and colon cancer as well. In these cases, the pre-treatment presence of tumor cells is prognostic of a poor outcome. Further-more, in metastatic breast cancer, the presence of tumor cells at the end of the first course of chemotherapy, is predictive of treatment failure. Another CTC test (Adnagen, Breast Cancer Cell Select and Detect) uses multi-antigen cell capture with antibody labeled magnetic beads, followed by RT-PCR characterization of selected genes. This and other new CTC tests may compliment the Cell Search assay for tumor cell detection in blood. 

12:30-1:00 Functional Genomics Identifies ABCC3 as a Biomarker of Taxane Resistance in HER2 Amplified Breast Cancer
Mark R. Lackner, Ph.D., Scientist, Development Oncology Diagnostics, Genentech Inc.

1:00-1:30 Discovery of Protein Biomarkers of Prostate Cancer 
Joanna Hunter, Ph.D., Director, Protein Analysis, Caprion Proteomics Inc. 
Proteomic profiling using mass spectrometry has been applied to a study of human prostate cancer disease markers. A global proteomic approach was used to identify low abundance, tissue specific protein biomarkers contained in the lumen of the Golgi in the tissue of origin. These proteins are destined to be released into the blood but are highly concentrated in the Golgi, prior to release, making them more easily detectable by mass spectrometry. Golgi and other related vesicles were isolated from human prostate tumors and associated normal tissue from the same patients. Proteins that were up-regulated in the lumen of the Golgi from the tumor were identified, and included most of the known prostate tumor secreted markers as well as several unexpected bio-marker candidates. Included among the sixty differentially expressed proteins were the known markers PSA, KLK2, MIF, and ACPP, all four of which are in the 1 ng/ml range in blood. Immunoassays of two known secreted proteins, MIF and PSA, in the blood of the same patients, demonstrate that the plasma concentration of these proteins is directly correlated to their observed level in the tumor Golgi. 

1:30-2:00 Networking Refreshment Break

2:00-2:30 Imaging MALDI vs. Histologic Imaging of Cancer of the Colon: A New Diagnostic Paradigm
Paul H. Pevsner, M.D., Research Associate Professor of Pharmacology, New York University School of Medicine
Imaging of colorectal carcinoma biopsies by histology and imaging MALDI revealed chemical margins beyond the traditional margins identified by histopathology. The tumor biomarkers in the chemical margins were confirmed by protein extraction. The same proteins were found in the histologic tumor and chemical margins beyond the tumor. The chemical margin represents metastatic disease not identified on the histopathology.

2:30-3:00 Discovery and Validation of DNA Methylation-Based Biomarkers for Early Detection of Colorectal Cancer in Plasma
Cathy Lofton-Day, Ph.D., Vice President, Molecular Biology, Diagnostics, Epigenomics, Inc. 
Detection of colorectal cancer (CRC) at early stages has been shown to greatly decrease mortality from the dis-ease. Availability of a blood-based test for CRC is expected to improve screening compliance in the general population. Through methylation-sensitive, restriction enzyme based marker discovery we identified a region of the Septin 9 (SEPT9) gene that is methylated in over 90% of colorectal cancer tissues with little or no methyla-tion in normal colon tissue or other controls. Our process of biomarker development including real-time assay and preanalytics development, and successful application of the SEPT9 methylation biomarker to the specific detection of tumor DNA in multiple studies of plasma from CRC patients and controls will be described.

12:00-3:00 Executive ThinkTank*
(*Premium Package registration required.)

12:00-12:30 Participant Introductions

12:30-12:50 Biomarkers: A Distraction or an Essential Drug Development Tool?
Nicholas C. Dracopoli, Ph.D., Vice President, Biomarkers, Centocor R&D, Johnson & Johnson
Investment in biomarkers has increased over the last few years while the numbers of new drug approvals has declined and the overall cost of pharmaceutical R&D has continued to increase. This suggests the increased scientific knowledge about the drug and its target is not being effectively converted into practical impact on the drug development and regulatory approval process. Can this paradox be resolved? Can biomarkers be used to reduce attrition and lower the overall costs of drug development? Or, do biomarkers just add cost and complexity without providing real time impact on the pharmaceutical development process? This presentation will include some examples of successful use of biomarkers, and make the case that the selective use of biomarkers is necessary, if not sufficient, for cost-effective drug development.

12:50-1:10 Can Biomarkers Be Tools in Decision Making or is This Wishful Thinking?
Geert Kolvenbag, M.D., Ph.D., Executive Director, Development, Emerging Oncology and Infection Brands, AstraZeneca 
With increasing resource pressure, drug developers need to make effective and informed go/no-go decisions as early as possible in development. This allows the best compounds to move ahead with adequate resource sup-port. Biomarkers are increasingly used as a tool in this decision making process. There are examples where bio-marker data have indeed facilitated early decision making. However, in contrast, there are also examples that biomarker data turned out to be unrelated to clinical outcome. Hence, the challenge remains to find the right tools for informed decision making in early drug development.

1:10-1:30 Generating Returns on Biomarker Research Investments - Transitioning from Biomarker Research to Product Development and Commercialization
Michael Stocum, Managing Director, Personalized Medicine Partners
This presentation will focus on the key aspects of successful biomarker programs in pharma and the process of how to make decisions regarding progression of these to clinical laboratory service tests and diagnostics. The presentation will highlight existing examples of successes and also discuss the potential risks and pitfalls in de-veloping such products. Lastly, the presentation will discuss potential business relationships and structures to enable co-development of such products to add value to both the medicine and the test.

1:30-3:00 Discussion with all Participants
Discussion Topics Include:

• Which types of biomarkers should be developed at various stages in the drug pipeline?
• What strategies help translate biomarkers from preclinical to clinical development?
• What type of biomarker data should lead to terminating a target or a compound? What type of data should lead to increased investment in a compound?
• How should biomarker data be weighed against “traditional” safety and efficacy data? Can 
  “general” toxicity biomarkers be re-used across programs?
• What level of validation is required for which types of decisions?
• Are biomarker data from healthy volunteers useful in assessing efficacy in patients?
• What regulatory guidance is needed?
• What are the current biomarker “best practices” in place at big pharma?
• How to estimate and measure ROI on biomarkers?
• How to manage risk in biomarker development? What validation and monitoring practices should be in place?
• Where is the value of using biomarkers in decision making? What is the cost of mistakes? Which biomarkers are the highest-value or highest-risk?
• Which biomarkers should big pharma develop independently and which can be co-developed in a cost-sharing model as pre-competitive information?
• What are the current obstacles in biomarker implementation?