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The Science of BioBanking - Day 2

Conference Proceeding CD Now Available
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Tuesday, December 7, 2010


7:30am Breakfast Presentation (Sponsorship Opportunity Available)
Contact Jon Stroup at 781-972-5483 or for information

8:15 BioBanking Brainstorming Breakthroughs 

Grab a cup of coffee and join a table discussion. These focused groups are designed for conference attendees to discuss important and interesting topics related to biospecimens from procurement, preservation, biomolecular extraction, and biomarkers. These are moderated discussions with brainstorming and interactive problem solving, allowing conference participants from diverse areas to exchange ideas, experiences, and develop future collaborations around a focused topic.


Utilization of Biospecimens for Drug Development

9:15 Chairperson’s Opening Remarks

9:20 Access to High Quality, Well-Annotated Specimens as a Critical Success Factor for Successful Registration and Commercialization of Candidate Drugs and Diagnostics

John C. Bloom, V.M.D., Ph.D., President, Bloom Consulting Services, LLC; Special Government Employee, FDA

Access to appropriately collected, annotated and stored specimens from clinical trial subjects, as well as those obtained from external biorepositories and clinical services, are increasingly critical to the successful development, registration and commercialization of today’s candidate drugs and diagnostics. In addition to providing a means for new target identification, validation and characterization, applications include the prospective and retrospective development of novel biomarkers and diagnostics that predict efficacy and/or toxicity, and enable patient stratification, regulatory/safety risk management, product differentiation and personalized medicine. Annotated specimens banked from clinical trials are the exclusive source of much of the above data; they also provide an important “insurance policy” that enables sponsors to address claims relating to genetic and other associations with outcomes of their marketed drugs. As such, they are irreplaceable and invaluable. Despite the financial, logistical, organizational and political challenges routine banking and specimen acquisition pose, the value proposition is compelling and one that drug hunters today cannot ignore

9:50 Early Learnings in Integrating Second Generation Sequencing with Molecular Pathology in the Development of Novel Cancer Chemotherapeutics

Keith Robison, Ph.D., Lead Senior Scientist, Bioinformatics, Infinity Pharmaceuticals, Inc.

This presentation will review the challenges faced in applying second generation sequencing to pre-clinical and clinical samples for informing clinical development of compounds with novel mechanism-of-action. These would include challenges in obtaining high-quality DNA from suitably consented samples, considerations in the choice of targeted sequencing strategies and downstream informatics. Vignettes from 1-3 pilot studies using different targeted sequencing technologies will be presented.

10:20 Drug Rescue and the Value of BiobankingSponsored by
Gentris web

L. Scott Clark, Ph.D., Chief Scientific Officer, Gentris Corporation

For every 5,000 drug candidates that enter pre-clinical testing, only one will receive FDA approval. Pharmaceutical organizations are under pressure to reduce costs and address key reasons for drug failure – adverse drug reactions, lack of efficacy, and unfavorable pharmacokinetics/drug metabolism properties. Banking a consented pharmacogenomic sample becomes invaluable for any of the above scenarios. Analysis or re-analysis of stored samples can rescue a failed drug by eliminating re-recruiting, re-consenting, and re-enrolling patients.

10:35 Morning Coffee Break with Exhibit and Poster Viewing

Leveraging Biospecimens for Biomarker Signatures 

11:15 Unlocking Tissue Proteomics for Cancer Biomarker Discovery

Cheng S. Lee, Ph.D., Associate Professor, Chemistry and Biochemistry, University of Maryland, College Park

There is increasing acceptance that relating tissue morphology with data obtained from various molecular analyses is critically important. Proteomic profiling of archived formalin-fixed tissues for which there is corresponding clinical information has great potential for biomarker discovery. Oncoproteomic studies of paired primary and recurrent (post-chemotherapy) ovarian high grade serous carcinomas from nine ovarian cancer patients will be presented. Results show that NF-kB and STAT5 inhibitors sensitize carboplatin-resistant cells and suggest that such inhibitors can be used to benefit patients with carboplatin-resistant recurrent ovarian cancer.

11:45 The Potential of Blood-Based Biomarkers in the Management of Alzheimer’s Disease

Olivier Charles Maes, Ph.D., Research Scientist, Lady Davis Institute for Medical Research

Alzheimer’s disease (AD) is a degenerative brain disorder that affects peripheral tissues such as blood constituents. Biomarkers in AD blood may reflect degenerative processes within the central nervous system and provide insights into the pathogenesis of AD. Noninvasive blood specimens are easily obtainable and may facilitate disease diagnosis and progression. The delineation of blood-based biomarkers in AD will also provide prognostication in preclinical stages as well as novel therapeutic leads and reflect efficacy of treatment for this devastating disease.

12:15 pm Close of Morning Session


12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own
Contact Jon Stroup at 781-972-5483 or for information


Preparing the Biospecimen – Biomolecular Processing and Extraction

2:00 Chairperson’s Opening Remarks

2:05 Realistic and Cost-Effective Strategies to Extend ‘Next-Tech Assays’ to Tissue Samples

Galen Hostetter, M.D., Associate Investigator, Integrated Cancer Genomics Division; Head, Colorectal Cancer Research; Director, Tissue Microarray Core, TGen

Genomic and epigenomic technologies, such as array comparative genomic hybridization (aCGH), CpG island hypermethylation and microRNA profiling are increasingly utilized in clinical samples.  Historically, genome and transcriptome profiles were limited to large fresh-frozen tumors where intact DNA and RNA could be readily extracted.   Our research activities have focused on extending discovery-based array CGH surveys using fresh frozen and paraffin split sample aliquots and more recently to the methylome surveys utilizing same patient tumor and normal FFPE samples.   We review DNA extraction and processing steps and the quantitative and qualitative measures to ensure suitable template for downstream applications.

2:35 Proteomic Sample Collection, Processing, and Storage for Cancer Biomarker Research

Farid E. Ahmed, Ph.D., Director, GEM Tox Consultants & Labs, Inc.

This presentation will describe methods of proteomic sample collection, processing and storage with focus on techniques employed for cancer biomarker discovery. Technologies employing cold chain logistics biostorage will be elucidated. Emphasis will be placed on the relevance of these approaches to personalized medicine and cancer biomarker discovery.

3:05 Optimizing a Proteomics Platform for Urine and Other Biofluids Biomarker Discovery

Towia A. Libermann, Ph.D., Associate Professor, Medicine, Beth Israel Deaconess Medical Center

Proteomics technologies are rapidly evolving over the last years and are providing the tools for biomarker discovery in human diseases. While mass spectrometry until recently had major limitations with regard to quantitation, sensitivity and throughput when applied to larger sets of clinical samples, recent technological developments have resulted in significant enhancements that make clinical proteomics feasible. Nevertheless, biospecimen collection, storage, and processing are additional critical parameters for optimal biomarker discovery. We have explored various parameters with regard to urine and other biofluids for optimizing quantitative proteomics approaches for biomarker discovery. Sample preparation and extraction methods for enhancing reproducibility and protein detection will be discussed.

3:35 Refreshment Break with Exhibit and Poster Viewing

4:00 The Proteomic Sample: Factors that Impact Accuracy and Variability in Mass Spectrometry Based Measurements

Iulia M. Lazar, Ph.D., Associate Professor, Biological Sciences, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University

Large scale proteomic experiments conducted with mass spectrometry instrumentation involve multiple level decisions that affect sample collection, storage, preparation, analysis and computational data processing. This presentation will review some of the critical steps that have been found to impact severely the outcome of such experiments and the interpretation of results. Relevant examples, compiled from data generated by the analysis of cancer cell lines, will be discussed. Technological advances that could improve the accuracy and minimize the variability of mass spectrometry measurements will be evaluated.

4:30 Sponsored Presentations (Opportunities Available)
Contact Jon Stroup at 781-972-5483 or for information

5:00 Utility of Biospecimens for Epidemiologic Research: Experience from the PLCO Trial

Wen-Yi Huang, Ph.D., Epidemiologist, Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS

Macromolecules extracted from biospecimens can be used to assess genetic, epigenetic, transcriptional, biochemical, serological, pathological and other biomarkers, useful for investigating the causes of disease. Pre-diagnostic and serial biospecimens collected in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Trial, along with participants’ questionnaire and clinical data, have been utilized to yield high impact research findings and continue to be an open resource for researchers.

5:30 Dedicated Poster Viewing with Wine & Cheese Reception in Exhibit Hall

6:00 Close of Day

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