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Short Courses | Day 1 | Day 2 | Day 3 | Download Brochure Thursday, February 4
PERSONALIZING THERAPY: SERUM BIOMARKERS 8:25 AM Chairperson’s Remarks Josip Blonder, M.D., Sr Research Scientist; Head, Quantitative Proteomics, NCI Frederick 8:30 Personalized Oncoproteomics for Cancer Biomarker Discovery: Application to Renal Cell Carcinoma
Discovery of diagnostic, therapeutic and prognostic markers is central to personalized treatment of cancer. Thus, proteomic approaches capable of characterizing the patient’s tumor phenotype using clinically relevant specimens are critically needed. A method that relies on tissue-directed oncoproteomics is described and applied for cancer biomarker discovery in the plasma of a patient diagnosed with renal cell carcinoma. 9:00 Protein Quantification Through Targeted Mass Spectrometry: The Way Out of Biomarker Purgatory? Steven A. Carr, Ph.D., Director, Proteomics, The Broad Institute of MIT and Harvard Immunoassays are widely used to measure protein biomarkers in patient blood, but useful antibody reagents do not exist for the vast majority of proteins. We are addressing this serious barrier by developing targeted assay methods employing mass spectrometry to screen and quantify low abundance proteins in plasma. This presentation will focus on the latest developments and applications of these technologies. 9:30 Mass Spec for Prostate Biomarkers, Assessing Aggressive vs. Non-Aggressive Prostate Cancer
Three types of prostate cancer related genetic variants have been found from genome-wide association studies, including those associated with overall prostate cancer risk, aggressive prostate cancer risk, and higher baseline PSA levels. These genetic variants may have potential clinical utility. However, further studies are needed to assess their clinical validity and clinical utility.
10:00 Sponsored Presentation (Sponsorship Opportunity Available) 10:30 Poster Competition Refreshment Break & Raffles in the Exhibit Hall 11:20 Metabolomic Analysis of Prostate Cancer Progression
Prostate cancer is the second most common cause of cancer-related death in men in the United States and afflicts one out of nine of those over the age of 65. There is an urgent need to develop biomarkers that can supplement PSA and increase its specificity for prostate cancer. The advent of high throughput profiling strategies has allowed scientists to look at global changes in genome, proteome and metabolome. Metabolomics, unlike genomics and proteomics, is a young science that has the potential to radically alter the future of healthcare, drug discovery, and drug delivery. It is the single best window into the cellular state discovered to date. Like the other omics-style sciences, where genomics is best understood as defining the genetic potential, transcriptomics is a window into the future (desired) direction of the cellular activity, and proteomics is a window to the functional potential of the cell; metabolomics, the omics science of metabolism, is the only window into the current and actual state of the cell (or by extension, organism) at a specific point in time. Recently we have profiled the metabolome in prostate cancer progression using a combination of GC and LC chromatography. Our study quantified the levels of >1000 metabolites across 250 biospecimens. Results of the profiling study revealed elevated levels of sarcosine or N-methyl glycine to be associated with advanced prostate cancer. Importantly components of sarcosine pathway were found to regulate prostate cancer aggressivity. In addition to sarcosine we have defined additional metabolites that are being characterized in the context of prostate cancer progression. Our long term objective is to define a multiplex panel of metabolomic markers for prostate cancer progression. 11:45 Circulating Tumor Cells: From Enumeration to Comprehensive Characterization
Circulating tumor cells (CTC) are very rare and consist of about 1 in 108 or 109 cells in blood drawn from some patients with metastatic cancer. Enumeration of CTCs has been shown to have prognostic value for patients with metastatic breast prostate and colorectal cancer, and is being evaluated to determine if a treatment-related reduction in CTC counts is predictive of therapeutic response. Comprehensive characterization (DNA, RNA and protein) of CTCs will significantly add to the value of CTC enumeration tests, and enable serial monitoring of CTCs for molecular changes occurring during disease progression and as a response to therapy. This presentation will review new approaches for the isolation and characterization of CTCs, and discuss how CTC-derived biomarkers will become a critical factor in the development of personalized treatment strategies in oncology. 12:10 PM Progress in Noninvasive Detection of Nucleic Acid Biomarkers Charles R. Cantor, Ph.D., CSO, Sequenom, Inc. Procedures have been developed to enhance the collection of RNA and DNA fragments that enter the peripheral circulation as a result of apoptosis. These include optimized methods of recovering small fragments, amplifying them and then detecting and quantifying sequence characteristics by nucleic acid mass spectrometry. The methods show promise in noninvasive prenatal diagnostics, tumor detection and characterization, and infectious disease agent identification. The overall process is considerably more sensitive and precise than commonly used alternatives. 12:35 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own 1:45 Ice Cream Refreshment Break in the Exhibit Hall
PLENARY KEYNOTE SESSION 2:15 Plenary Keynote Introduction 2:25 Chips, Clones and Living Beyond 100
As information technologies and life sciences continue to converge, new business opportunities and challenges will arise for the field of diagnostics and beyond. This keynote reviews the deeper forces shaping the future of the biosciences, from social and economic to technological and political, including the stresses they will introduce for existing business models and healthcare. Not only will bioconvergence introduce new products, services and competitors, it may create entirely new industries on a scale larger than the computer revolution has to date. Several broad scenarios will be painted for the state of the biosciences in 2025 and the forces that might take us there, summarizing a multi-year strategy study conducted and supervised by the speaker at the Wharton school. 3:05 Refreshment Break in the Exhibit Hall
NEXTGEN SEQUENCING AS A CLINICAL TOOL 3:45 Chairperson’s Remarks 3:50 Enabling Personalized Medicine: The Growing Role of Next Generation Sequencing German Pihan, M.D., Department of Pathology, Beth Israel Deaconess Medical Center Ready access to the genome sequence of a patient is arguably the single most important factor in the implementation of personalized medicine. The recent development of massive parallel sequencing technologies promise to make personalized medicine soon a reality. Here I review the technological state-of-the-art as well as the clinical areas where massive parallel sequencing may have the greatest and most immediate impact. 4:20 Keynote Presentation
Henry A. Erlich, Ph.D., VP, Discovery Research, Human Genetics, Roche Molecular Systems, Inc. The HLA class I and class II loci are the most polymorphic genes in the human genome. In current methods for HLA typing, both alleles of a heterozygote are amplified and typed or sequenced simultaneously, often making it difficult to unambiguously determine the sequence of the two alleles. Next-generation sequencing methods clonally propagate in parallel millions of single DNA molecules which are then also sequenced in parallel. . The clonal sequence read lengths of > 250 bases achieved by the 454 GSFLX system make possible setting the phase of the linked polymorphisms within an exon and thus the unambiguous determination of the sequence of each HLA allele.. Highly multiplexed amplicon sequencing is facilitated by the use of sample-specific internal sequence tags (multiplex identification tags or MIDs) in the primers that allow pooling of samples (24 or 48 per run) yet maintain the ability to assign sequences to specific individuals. We have incorporated an HLA typing software application developed by Conexio Genomics that assigns HLA genotypes for these 7 loci (HLA-A, -B, -C, DRB1, DQA1, DQB1, DPB1), as well as for DRB3, DRB4, and DRB5 from 454 sequence data. The potential of this HLA sequencing system to analyze chimeric mixtures is demonstrated by the detection of a rare HLA-B allele in a mixture of two homozygous cell lines (1/100), as well as by the detection of the rare non-transmitted maternal allele present in the blood of a Severe Combined Immunodeficiency Disease Syndrome (SCIDS) patient. 4:50 Next Generation Sequencing for Hypertrophic Cardiomyopathy Diagnostics Karl V. Voelkerding, M.D., Associate Professor of Pathology, University of Utah and Medical Director for Advanced Technology, ARUP Laboratories Hypertrophic cardiomyopathy is an autosomal dominant disorder of cardiac sarcomere structure and function leading to multiple cardiac conditions. At least 16 genes with over 450 mutations have been implicated in HCM. We have currently designed and tested a next generation sequencing approach for the analysis of this multi-gene disorder and are refining our approach for diagnostic application. 5:20 HIV Dynamics Taught by Sequencing Ramy Arnaout, M.D., DPhil., Associate Director, Clinical Microbiology, BIDMC Staff Pathologist, Department of Pathology, BIDMC and Harvard Medical School, Beth Israel Deaconess Medical Center High-throughput sequencing platforms provide an approach for detecting rare HIV-1 variants and documenting more fully quasispecies diversity. We applied this technology to understand viral dynamics at the sequence level associated with antiviral treatment failure. Failure was associated with extreme, rapid shifts in population frequencies toward specific resistant forms, and deep sequencing provided a detailed view of the rapid evolutionary impact of selection. 5:50 Close of Day
Short Courses | Day 1 | Day 2 | Day 3 | Download Brochure |
Josip Blonder, M.D., Sr Research Scientist; Head, Quantitative
Proteomics, NCI Frederick 
Jianfeng Xu, M.D., Ph.D., Professor, Wake Forest University
School of Medicine 
Arun Sreekumar, Ph.D., Molecular Oncology Program, Medical
College of Georgia 
Nicholas C. Dracopoli, Ph.D., VP, Biomarkers, Centocor
R&D, Inc., Johnson & Johnson 
Paul J.H. Schoemaker, Ph.D., M.B.A., Chairman and Chief Executive Officer,
Decision Strategies International, Inc.; Research Director, Mack Center for
Technological Innovation, The Wharton School; Adjunct Professor of Marketing,
The Wharton School Adjunct Professor, Wharton School of Business
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