FAST Congress
Archived Content

Clinical Biomarkers


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Wednesday, September 19

» Opening Plenary Session 

2:00-3:00 Main Conference Registration

3:00-3:10 Welcoming Remarks from Conference Director

Julia Boguslavsky, Executive Director, Conferences, Cambridge Healthtech Institute

Strategies to Accelerate Development and Advance Personalized Therapy (ADAPT) 

3:10-3:15 Chairperson's Opening Remarks

3:15-3:45 Rules, Tools and Data Pools: The Critical Path's Recipe for Speeding Drug Development

Carolyn ComptonCarolyn Compton, M.D., Ph.D., President & CEO, Critical Path Institute

Both regulatory agencies and the medical products industry recognize the need for new biomarkers and methods to speed the development and delivery of effective, safe medicines to patients. However, developing consensus on the utility of new biomarkers and establishing a process for putting them into routine practice in medical product development and regulatory decision making is a complex undertaking. In 2009 and 2010, respectively, the European Medicines Agency and the FDA released guidance that describes a voluntary pathway for "qualification" of novel drug development tools or methods. Determining the relative advantages/disadvantages and evidentiary standards required for regulatory "qualification," applying a novel biomarker on a specific drug development program, or submitting an application for a diagnostic device are challenging tasks. The Critical Path Institute (C-Path) acts as a trusted third party to lead six pre-competitive global consortia that, with the cooperation of the FDA, develop and qualify molecular and imaging biomarkers as well as patient-reported outcomes instruments for specific contexts of use in medical product development. Several C-Path consortia use Clinical Data Interchange Standards Consortium disease area data standards in constructing clinical trial databases from which disease progression models and virtual clinical trial simulations are developed. Specific examples from these consortia will be utilized to illustrate the power of pre-competitive collaboration in the generation and qualification of drug development tools.

3:45-4:15 Technology Transformation at FDA: Driving Efficiency and Unleashing Innovation

Eric-PerakslisEric D. Perakslis, Ph.D., Chief Information Officer and Chief Scientist, Informatics, U.S. Food and Drug Administration

The U.S. Food and Drug Administration has recently taken significant steps to modernize and improve its information technology and informatics capabilities.  The resulting infrastructure, architecture, innovation pathways and data sharing initiatives are intended to ease regulatory burden on innovators while maintaining the highest quality standards. In this talk, Eric Perakslis, Ph.D., the Chief Information Officer and Chief Scientist for Informatics at FDA, will discuss these initiatives in detail and will provide success examples, recent progress and future directions.

4:15-4:45 Turning an Active Compound into a Personalized Medicine: Do Biomarkers Help or Hinder?

Geert-KolvenbagGeert Kolvenbag, M.D., Ph.D., Global Product Vice President, AstraZeneca

The co-development of drug and biomarker has several inherent risk and challenges. In addition the expectations and demands of the oncology community have increased over the last years. These challenges will be illustrated by a case study of a very active compound destined for a fast development program as a personalized medicine, but running into scientific, diagnostic and development challenges. This experience creates questions for development of drugs and diagnostics today and in the future.

4:45-5:15 Strategies to De-Risk Drug Development Utilizing Biomarkers in Early Clinical Trials

Scott-KennedyScott Kennedy, Ph.D., Global Head, Biomarker Development, Novartis Institutes for BioMedical Research, Inc.

Other than recent examples in oncology, the emerging field of personalized medicine has yet to live up to its promise of enabling more rapid, efficient drug development and providing customized therapies to patients. This presentation will exemplify and discuss how leveraging biomarkers which inform a biological understanding of targeted and disease pathways can increase the success of early clinical development.  These biologically relevant markers can also enable the identification and treatment of parallel disease populations and serve as stratification or response markers for later stage development. This presentation will also discuss several of the challenges that this paradigm presents.

5:15-5:45 Implementing a Personalized Medicine Strategy: Is There Light at the End of the Tunnel?

Jeremy BartonJeremy Barton, M.D., Vice President, Head of Oncology Clinical Research, Pfizer

Personalized medicine, the practice of tailoring treatment to individual characteristics of the patient, has emerged as a major force in oncology in the last decade with the expectation of significant improvement in safety and efficacy of therapeutics. The ultimate success of this paradigm is dependent on a variety of factors. The choice of drug target, selection of patients by companion diagnostic, regulatory authority acceptance of novel trial designs which best serve this strategy, improved health care information technology, insurance coverage and reimbursement are just a few of the important variables in the equation. This presentation will provide an overview of the current situation and discuss factors which will impact future progress in the field.

5:45-6:45 Welcome Reception in the Exhibit Hall with Poster Viewing

Thursday, September 20

7:30-8:15 am Morning Coffee or Sponsored Breakfast Presentation (Opportunity Available)

Contact Ilana Quigley at or 781-972-5457

Case Studies in Drug-Diagnostic Co-Development 

8:30-8:55 Co-Development of Vemurafenib and the cobas® BRAF Mutation Test

Walter H. Koch, Ph.D., Vice President and Head of Global Research, Roche Molecular Diagnostics

Categorization of cancers based on oncogenic genomic alterations has identified numerous new kinase drug targets. Development of targeted kinase inhibitor therapies alongside companion diagnostics that will identify patients most likely to receive benefit represents a new model for drug development, and portends increased success rates for therapeutics, with decreased development times and associated costs. The co-development of vemurafenib (ZelborafTM) and the cobas® 4800 BRAF V600 mutation test will be presented from the diagnostics perspective. This focused and integrated process resulted in the first personalized medicine for the treatment of metastatic melanoma less than five years after the Investigational New Drug Application was filed.

8:55-9:20 Integrating a Companion Diagnostic into the Clinical Development of Crizotinib

Ian Taylor, Ph.D., Senior Director, Translational Oncology, Pfizer

Fully integrating a diagnostic test into the development of crizotinib (XalkoriTM) for treatment of NSCLC patients presented technical, clinical and regulatory challenges as well as opportunities to conduct smaller clinical trials with a greater chance of those trials being successful by appropriately identifying a patient population expected to benefit from crizotinib treatment.  This presentation will describe the novel approaches as well as close collaboration between Pfizer, Abbott, CDER, and CDRH that resulted in the simultaneous submission and approval of a new drug-diagnostics combination.

9:20-9:45 Creating a Framework for Personalized Medicine in CF: The Kalydeco® Experience

Preston W. Campbell, III, M.D., Executive Vice President for Medical Affairs, Cystic Fibrosis Foundation

The Therapeutics Development Program of the Cystic Fibrosis Program will be highlighted as a model of non-profit-industry collaboration. Kalydeco was discovered and developed through this program and was recently approved for the treatment of persons with CF that carry at least one copy of the CFTR gene mutation G551D, less than 5% of the US CF population. Physical-chemical studies of CFTR mutation phenotypes suggest that there are patients carrying many other, but less prevalent, CFTR mutations that may also benefit from Kalydeco therapy. As an advocacy organization, our challenge is to support processes by which every patient that has a reasonable chance of benefiting from a therapy be given the opportunity to do so. Our approach will be discussed.

9:45-10:45 Coffee Break in the Exhibit Hall with Poster Viewing

Technology Showcase 

Caprion10:45-11:15 Strategies for Clinical Biomarker Discovery and Verification with Mass Spectrometry-Based Proteomics

Laura McIntosh, Ph.D., Senior Director, Caprion Proteomics, Inc.

Three successful strategies for the discovery and verification of clinical biomarkers have been applied to a wide range of diseases and candidate therapies. Case studies will be presented distinguishing malignant from benign lung nodules, active from latent TB and responders from non-responders in an H5N1 avian flu vaccine trial.

BioAgilytix11:15-11:30 Lot Bridging Considerations for Single and Multiplex Immunoassay Kits in Biomarker StudiesAfshin Safavi, Ph.D., Founder & Senior Vice President, Bioanalytical Operations, BioAgilytix LabsBiomarker analysis has become a common practice by many pharmaceutical and biotechnology companies to help PK/PD modeling.  The reliability of outcomes is heavily influenced by the quality of the kits used to support the studies. The goal of this presentation is to increase awareness of the bioanalytical considerations that are involved in bridging immunoassay assay kit lots.

HTG Logo Small11:30-12:00 Extraction-free mRNA Gene Expression Analysis in FFPE:  Analytical, Clinical, and Regulatory Considerations for an IVD

Sam RuaSam Rua, Vice President, Regulatory Affairs & Quality Systems, HTG Molecular Diagnostics, Inc.

Traditional methods for gene expression analysis involve having to extract nucleic acids from biological samples, with extraction efficiency dependencies on the sample type, extraction method, and operator proficiency.  This talk will cover assay performance and regulatory aspects of bringing an extraction-free mRNA expression IVD to market. 

12:00-1:30 Enjoy Lunch on Your Own

Integrating Biomarkers into Clinical Trials 

1:30-1:35 Chairperson’s Opening Remarks

1:35-2:00 Biomarkers in the Clinic: How to Find Them and Apply Them in Clinical Trials

Suso Platero, Ph.D., Director, Oncology Biomarkers, Janssen Pharmaceuticals

Finding biomarkers is relatively straightforward. Nowadays, with the advent of next-gen sequencing, transcriptional profiling, proteomics and other genomics technologies, the scientific literature is full of biomarkers for different targets and pathways. Now, finding biomarkers that are useful in a clinical setting is another task altogether much more difficult. Here we encountered several problems; does our drug of choice modify the biomarker that we want to focus on? Does the presence of the biomarker have any consequences in the results obtained by treating the patients with the drug we want to test? Do we have a clinically relevant test that we can apply to our patients? I will show several examples in which we have discovered pharmacodynamics biomarkers, markers that change upon compound treatment, and predictive biomarkers, markers that will predict response or resistance in the patients. Furthermore, I will show how we have taken those biomarkers and develop clinically relevant tests and then apply them in clinical trials.

2:00-2:25 Fit-for-Purpose Biomarker Development and Applications in CNS Clinical Trials: Is the Buzz Ready for Primetime?

Susan E. Ward, Ph.D., Senior Clinical Program Leader, Translational and Experimental Medicine, Biogen Idec

The use of biomarkers in CNS clinical development has increased dramatically over the last few years in part to mitigate the risk as a number of late stage CNS trials have failed. Biomarkers can be used throughout the drug development lifecycle to understand the mechanism of action or demonstrate target engagement in early phase trials; to stratify and enrich study populations or predict response to a compound in later stage trials. With the inclusion of biomarkers, the complexity of CNS trials has increased as well as the operational challenges, especially for large multi-center trials. This session will discuss the value of using biomarkers in clinical trials and the inherent challenges that this novel technology may introduce.

2:25-2:50 Pharmacodynamic Biomarkers in Oncology Early Drug Development

Monica Motwani, Ph.D., Director, Oncology Biomarkers, GlaxoSmithKline

Efficient and successful transition of a targeted agent through the drug development pipeline requires robust pharmacodynamic (PD) biomarker measurement during initial clinical development. While it is critical to have a scientifically and analytically validated biomarker, obtaining a high quality sample is imperative to obtaining quality data that will lead to a decision. In fact, the absence of high quality samples is one of the most significant roadblocks in successful integration of biomarker data in decision making. AACR-FDA-NCI Cancer Biomarkers Collaborative (CBC) in 2007 identified biospecimens as one of the eight critical areas for efficient and effective biomarker development. This presentation will focus on obtaining quality paired biopsies for PD analysis and lessons learned from prior studies.

2:50-3:15 Multiple Testing for Biomarker Discoveries and Subgroup Identification in Personalized Medicine

Jason C. Hsu, Ph.D., Research Fellow, Eli Lilly and Company; Emeritus Professor, Statistics, The Ohio State University

One form of personalized medicine is a drug targeting a subgroup of the patient population, which requires the drug and its companion diagnostic test be approved by the FDA simultaneously. To discover biomarkers predictive of efficacy, permutation multiple tests are often used. I will show the surprising result that unless a subtle model assumption holds, permutation multiple tests do not control Type I error rate. Once a small number of predictive biomarkers have been discovered, a technique more powerful than Closed Testing is available to simultaneously test for efficacy over the patient population and in subgroups. I will show Partition Testing simplifies multiple testing and gains power by recognizing logical relationship between the parameters. Confidence sets from Partition Testing can also resolve the controversial “consistency” criterion in subgroup identification.

3:15-4:15 Refreshment Break in the Exhibit Hall with Poster Viewing

Integrating Genomics into Personalized Therapy Development 

4:15-4:20 Chairperson’s Opening Remarks

4:20-4:45 Genetic Signatures and Their Use for Personalized Therapy

Paola Sebastiani, Ph.D., Professor, Biostatistics, Boston University

Genome-wide association studies have shown that the genetic basis of many diseases is complex, and this complexity has raised questions about the utility of genetic data for personalized therapy. I will describe an approach that can help dissect the genetic basis of complex traits. The method builds genetic risk profiles with large numbers of genetic variants, and uses cluster analysis to group them into genetic signatures. By examining the association between genetic signatures and sub-phenotypes of a trait, the method can identify genetic signatures linked to specific response to treatment. I will show examples from genetic traits with different heritability.

4:45-5:10 Next-Generation Sequencing in Drug Discovery

Joseph D. Szustakowski, Ph.D., Senior Group Head, Translational Medicine, Biomarker Development, and Bioinformatics, Novartis Institutes for Biomedical Research

Next-generation sequencing technologies and applications have seen rapid uptake in all facets of drug discovery. The inclusion of NGS platforms in our experimental armamentarium is enabling a host of experiments that were previously not tractable. Several NGS case studies will be reviewed with an emphasis on understanding and predicting how NGS will impact our clinical biomarker efforts.

5:10-5:35 Personalized Medicine: An Update on 1,985 Patients with Advanced Cancer at MD Anderson Cancer Center

Apostolia-Maria Tsimberidou, M.D., Ph.D., Associate Professor, Investigational Cancer Therapeutics, University of Texas, MD Anderson Cancer Center

We hypothesized that in Phase I clinical trials, use of targeted agents matched with tumor molecular aberrations would improve treatment outcomes. A targeted therapy was considered to be “matched” to a patient if at least one drug in the regimen was known to inhibit the functional activity of at least one of the patient’s mutations. In a 5-year period, 50% of patients who underwent tumor molecular profiling had a molecular aberration. Rates of response, time to treatment failure, and survival were higher in patients treated with matched Phase I therapy compared to those of patients treated with non-matched Phase I therapy. In patients treated with matched Phase I therapy, time to treatment failure was longer than on prior systemic therapy. These results continue to support use of a personalized molecular approach for patients with cancer. Complete molecular profiling to understand resistance mechanisms and new targeted agents are needed.

5:35-6:00 GliomaPredict – Translation from Transcriptomic Subtypes to Patient Bed

Aiguo Li, Ph.D., Senior Bioinformatician, NOB, National Cancer Institute, National Institutes of Health

We developed GliomaPredict, a tool that allows the fast and reliable assignment of glioma patients into one of six previously stratified subtypes based on sets of extensively validated classifiers. Our tool utilizes a principle component analysis (PCA)-based approach to generate a visual representation of the analyses, quantifies the confidence of the underlying subtype assessment and presents results as a printable PDF file. The GliomaPredict tool is implemented as a plugin application for the GenePattern framework. GliomaPredict provides a user-friendly, clinically applicable novel platform for instantly assigning transcriptomic subtype in patients with gliomas thereby aiding in clinical trial design and therapeutic decision making.

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