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Pre-Conference Workshops Monday, October 20, 2008 | PRE-CONFERENCE WORKSHOPS | DAY ONE | DAY TWO | DAY THREE | | |
| 7:30 | Registration and Morning Coffee |
| Workshop A: Meeting High Throughput Microarray Challenges | |
| Using microarray-based technologies in the HTP setting can present challenges that may become costly bottlenecks. This workshop will present strategies for addressing several of these challenges. | |
| 8:20 | Workshop Leader's Opening Remarks Mike Damore, Ph.D., Principal Scientist, Medical Sciences, Amgen |
| 8:30 | Challenges of Using Microarrays in a Clinical Trials Amgen has recently completed microarray analysis of PAXgene samples from a large clinical trial. Proper collection and handling of PAXgene tubes at clinical sites combined with appropriate RNA isolation protocols was shown to be important for the generation of microarray quality RNA. High throughput microarray labeling and hybridization was then required to successfully process the needed arrays prior to database lock. The difficulties and successes of these steps will be examined. Mike Damore, Ph.D., Principal Scientist, Medical Sciences, Amgen Inc. |
| 9:00 | CASE STUDY: High Throughput, High Density and Focused Custom Array Measurement of mRNA and miRNA From Any Sample, Including Archived FFPE mRNA/miRNA-based diagnostic assays of fixed (FFPE) tissue samples are needed. Development at both the high density array and focused assay stages is facilitated by testing archived FFPE samples, enabling retrospective studies on samples with known patient outcomes. Clustering of genes from high density array dose response data is also very powerful. Results from lysis-only, highly precise, custom microplate-based quantitative Nuclease Protection Assay analysis, performed as a high density array target identification assay will be discussed, together with validation using focused microplate-based assays. Bruce Seligmann, Founder, CSO and Vice President R&D, High Throughput Genomics, Inc. |
| 9:30 | CASE STUDY: Analysis by Design: First Steps to Improving Assay Performance An often overlooked tool to improve the relative performance of any high throughput technology is selection or alteration of the primary signal processing workflow to fit an assays specific intent. This talk will describe the benefits of designing primary signal processing steps (background, normalization, summarization, etc.) around the intended purpose of the experiment and how this can have a significant impact on concordance across platforms and overall performance. Charlie Johnson, Ph.D., President, BioMath Solutions |
| 10:00 | Networking Coffee Break |
| 11:00 | Panel Discussion with Workshop Speakers
Mike Damore, Ph.D., Principal Scientist, Medical Sciences, Amgen Inc. Bruce Seligmann, Founder, CSO, and Vice President, R&D, High Throughput Genomics, Inc. Charlie Johnson, Ph.D., President, BioMath Solutions |
| 11:30 | End of Workshop |
| Workshop B: In Silico Biomarker Validation | |
| Biomarker discovery and validation is a very complex, expensive and extensive undertaking. Systems biology as well as other in silico methods can link key existing data with an in silico context that can help to validate new biomarkers. This workshop will explore some of these approaches. | |
| 8:20 | Workshop Leader's Opening Remarks Lucila Ohno-Machado, Ph.D., Associate Professor, Radiology, Brigham and Women's Hospital, Harvard Medical School |
| 8:30 | CASE STUDY: Validation of Breast Cancer Biomarkers Determining whether a potential biomarker is specific for breast cancer or simply a marker of acute disease remains a challenge. Use of high-throughput gene expression and protein quantification technologies to characterize biomarkers has been widely reported. Many hypothetical biomarkers, based on little data, cannot be validated in further experiments. We describe the use of public repository data to develop a more robust biomarker prediction and validation process. Lucila Ohno-Machado, Ph.D., Associate Professor, Radiology, Brigham and Women's Hospital, Harvard Medical School |
| 9:15 | A Systems Biology Approach for Pathway Level Analysis A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all interactions taking place on various pathways. Existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results. Using a systems biology approach, we developed an impact analysis that includes classical statistics and also considers other important biological factors. Sorin Draghici, Ph.D., Associate Professor, Computer Sciences, Wayne State University |
| 10:00 | Networking Coffee Break |
| 11:00 | Panel Discussion with Workshop Speakers
Lucila Ohno-Machado, Ph.D., Associate Professor, Radiology, Brigham and Women's Hospital, Harvard Medical School Sorin Draghici, Ph.D., Associate Professor, Computer Sciences, Wayne State University |
| 11:30 | End of Workshop |
| Workshop C: Automated Sample Preparation Methods | |
| A potential limiting factor for any HTP process throughout discovery and validation is the efficient preparation of large numbers of samples. Methods for creating large quantities of unique reagents used in next generation sequencing and sample prep methods that feed into many different types of downstream assays will be discussed. | |
| 8:20 | Workshop Leader's Opening Remarks Joanne Horn, Ph.D., Staff Scientist, Microchip Biotechnologies |
| 8:30 | Use of Automated Template Preparation for Next-Generation DNA Sequencing To address upstream process bottlenecks, automated production of templates is being developed to feed next generation DNA sequencing platforms. One means for generating the large numbers of templates needed is to use massively parallel cartridge-microfluidics technologies that generate bead-bound bar-coded, single-stranded DNA templates. These templates are then subjected to emulsion-phase PCR that employs microfluidically-engineered emulsions followed by further downstream processing. The high throughput generation of templates addresses some of the upstream bottleneck issues. Joanne Horn, Ph.D., Staff Scientist, Microchip Biotechnologies |
| 9:15 | MALDI Imaging and Mass Spectrometry Identification of Colorectal Cancer Biomarkers MALDI (IMS) imaging of colorectal biomarkers in clinical tissue samples for proteomic classifi¬cation may provide greater sensitivity than histopathology, which alone may underestimate the extent of metaplastic or malignant disease. Verification of MALDI images requires either 'top-down' proteomics, FTMS or 'bottom-up' Hitachi nanoflow LCMS. A multiplexed sample preparation methodology was used to capture various analytes for these assays. MALDI imaging visualized protein loci in the tissue and the use of LCMS and FTMS protein identification verification of these biomarkers may be more reliable than either technique alone. Paul Pevsner, MD, Professor, Pharmacology, New York University School of Medicine |
| 10:00 | Networking Coffee Break |
| 11:00 | Panel Discussion with Workshop Speakers
Joanne Horn, Ph.D., Staff Scientist, Microchip Biotechnologies Paul Pevsner, MD, Professor, Pharmacology, New York University School of Medicine |
| 11:30 | End of Workshop |
|
Main Conference - Day One Monday, October 20, 2008 | PRE-CONFERENCE WORKSHOPS | DAY ONE | DAY TWO | DAY THREE | | |
| Sequencing and Detection Technologies | |
| Short RNA Prediction and Detection | |
| 12:30 | Chairperson's Remarks Winston Patrick Kuo, DDS, MS, DMSc, Director, Laboratory for Innovative Translational Technologies, Harvard School of Dental Medicine |
| Keynote Presentation | |
| 12:35 | Evidence of Expanded Regulatory Activity for Animal microRNAs MicroRNA studies with naturally-occurring binding sites have mostly supported a model by which animal microRNAs act primarily through the 3'UTR of the targeted transcripts, and lead to a sequence-dependent degradation of mRNA or disruption of mRNA translation. Recent work that revisits these observations and examines the possibility of other "natural" binding sites for microRNAs using both standard experimental approaches and computational methods will be discussed. Isidore Rigoutsos, Ph.D., Manager, Bioinformatics & Pattern Disc. Group, Comp. Biology Center, Deep Computing Institute, IBM Thomas J Watson Research Center |
| 1:20 | Achieving Accuracy in the Detection of microRNA using Microarray Methodologies MicroRNA microarray expression profiling depends on isolation and robust labeling of RNA samples including cultured cells, biopsy specimens and frozen or formalin-fixed paraffin embedded tissues. Scientists must also consider the implications of recent findings that some enzymatic labeling methods systematically miss specific microRNAs. Direct chemical labeling enables unbiased detection of microRNAs from all sample types and offers the potential for simultaneous labeling of multiple RNA species from a single sample. Shannon Bruse, Ph.D., Senior Scientist, Mirus Bio Corporation |
| 1:50 | Development and Applications of a Microarray Platform with On/Off Single Base Discrimination Genetic variation detection and discrimination are critical for identifying signature profiles for diagnostic and prognostic applications. The use of a novel covalent attachment chemistry, standard base composition oligonucleotide probes, and proprietary hybridization and wash buffers to achieve On/Off single base discrimination even among families of highly related sequences will be discussed. Application of this platform to miRNA expression profiling and virus serotyping will also be presented. Kerry B. Gunning, Ph.D., Senior Research Scientist, Molecular Genetics, Integrated DNA Technologies |
| Technology Workshop | |
| 2:20 | A Larger Multiplexed FAST® Quant™ Array
Immunoassay on protein microarrays is a powerful multiplex tool for quantitative determination of several cytokines. Whatman FAST Quant kits, for example, allow simultaneous measurement of 8-10 cytokines in each sample. A new FAST Slide-based array allows quantitative measurement of up to 40 cytokines and other analytes of interest. This 2-pad design allows quantitation of all the analytes in as little as 70 uL of serum. Data will be presented showing detection limits and dilutional recoveries.Michael A. Harvey, Ph.D., Director of Development, R&D, Whatman Inc., part of GE Healthcare |
| 3:00 | Networking Coffee Break |
| Assay Development | |
| 3:30 | Chairperson's Remarks Richard Rouse, Ph.D., HTS Resources |
| 3:35 | Using Next Generation Sequencing to identify new genetic markers: From somatic mutation detection to redefining whole genome association studies With over 250 publications, the Genome Sequencer FLX continues to provide new breakthroughs in the scientific community. Using the newly released Titanium reagents, the GS FLX is able to generate sequencing reads of 500 base pairs. This presentation will provide a brief introduction to the GS FLX and present overviews of recent studies that from sequencing whole human genomes to the detection of somatic mutations within tumor samples, to the comprehensive resequencing of 85 individuals over a 135 kb region of 8q24. Tom Jarvie, Ph D., Sr Product Manager, 454 Life Sciences |
| 4:05 | Casting a Wide Biomarker Net to Discern Novel Diagnostic Patterns Biomarker patterning using comprehensive, quantitative immunoassay panels provides robust tools for both drug development and diagnostic applications. These panels precisely measure hundreds of plasma analytes including biomarkers whose levels are indicative of cardiovascular risk, autoimmunity, metabolic disorders, cancer and inflammation as well as drug toxicity or efficacy. The application of these panels to appropriate disease and control samples elucidates the biomarker pattern of interest. Several successful examples of the application of this approach to identify novel diagnostic biomarker patterns will be presented. Ralph McDade, Ph.D., Strategic Development Officer, Rules Based Medicine, Inc. |
| 4:35 | CASE STUDY: Image Processing Techniques for Automated Sample Preparation using Piezoelectric Liquid Handling Robotics In broad terms, there are two approaches widely used for determining protein identification: 1) determine molecular weight using a mass spectrometer and 2) measure binding affinity with specific ligands (i.e., capture antibody and reverse phase microarrays). Related to both general techniques, we show how configuring a gantry system with piezoelectric dispense nozzles and imaging cameras can be effectively used for both applications. Richard Rouse, Ph.D., HTS Resources |
| 5:05 | End of Day One |
| Molecular Diagnostics | |
| Diagnostics Regulatory Dynamics | |
| 12:30 | Chairperson's Remarks Richard Naples, Vice President, Corporate Regulatory Affairs, BD Medical - Pharmaceutical Systems |
| Keynote Presentation | |
| 12:35 | Regulation of Emerging Diagnostics There are two paths to market for emerging diagnostics in the US. One path is through FDA premarket review, the other path to market is through CLIA '88 as a laboratory developed test. Earlier this year the Secretary's Advisory Committee on Genetics, Health, and Society (SACGHS) released a report that calls for changes in FDA and CLIA '88 requirements. Test developers must be aware of what the changing regulatory environment means to them and be engaged in the policy debate. Richard Naples, Vice President, Corporate Regulatory Affairs, BD Medical - Pharmaceutical Systems |
| 1:20 | Report of the Secretary's Advisory Committee on Genetics, Health, and Society on the Oversight of Genetic Testing The Secretary's Advisory Committee on Genetics, Health, and Society (SACGHS) issued its report, U.S. System of Oversight of Genetic Testing: A Response to the Charge of the Secretary of Health and Human Services, May 1, 2008. The report's recommendations— which address analytical validity, clinical validity, and clinical utility of genetic tests; the transparency of genetic testing; and the educational needs of health professionals and consumers—will be discussed during this session. Andrea Ferreira-Gonzalez, Ph.D., Chair, SACGHS Oversight Task Force |
| 1:50 | Panel Discussion
Richard Naples, Vice President Corporate Regulatory Affairs, BD Medical - Pharmaceutical Systems Andrea Ferreira-Gonzalez, Ph.D., Chair, SACGHS Oversight Task Force |
| 2:20 | Technology Workshop To learn more about sponsoring a Technology Workshop, please contact Sherry Johnson at (508) 614-1451 or sjohnson@ibcusa.com |
| 3:00 | Networking Coffee Break |
| Point-of-Care Diagnostics | |
| 3:30 | Chairperson's Remarks Matthew Lorence, Ph.D., MBA, Vice President, Marketing and Sales, TessArae, LLC |
| 3:35 | Nucleic Acid Technologies in Biomarker Discovery and Clinical Assays An active area of research focuses on identifying and verifying biomarkers useful for disease diagnostics and therapy selection. Nucleic acid-based technologies will play an important role in this research. This talk with outline some specific examples of nucleic acid based technologies utilized in cancer research and their application to biomarker and clinical assay research. Mickey Williams, Ph.D., Director, Pharmacogenomics, Roche Molecular Systems |
| 4:05 | Challenges Encountered during the Development of the BioSeeq-Vet Portable PCR System Smiths Detection has developed the BioSeeq®-Vet PCR System, a portable PCR instrument that performs automated sample preparation and LATE-PCR analysis. Nucleic acids are extracted and purified from samples by the Sample Preparation Unit (SPU), a single-use, self-contained sample preparation and PCR consumable. This presentation will discuss the challenges that were encountered during the development of the instrument and the automated Sample Preparation Unit and the solutions created to overcome those challenges. John W. Czajka, Ph.D., MBA, Vice President of Technology Acquisition, Smiths Detection |
| 4:35 | Infectious Disease Testing in the Point of Care Setting The demand for rapid diagnosis of infectious diseases is being met by a burgeoning of sophisticated technology. Rapid diagnosis is needed for patient management and for triaging patients that might need to be isolated. One technology, the Cepheid GeneXpert System, is the first to fully automate and integrate the steps needed for PCR based DNA testing. Cepheid offers PCR testing that can be applied in the point of care setting for MRSA surveillance and Group B Streptococcus testing. Susan M. Novak-Weekley, Ph.D., Director of Microbiology, SCPMG Regional Reference Laboratories |
| 5:05 | End of Day One |
| Biomarkers | |
| Biomarkers: Discovery, Validation & Efficacy | |
| 12:30 | Chairperson's Remarks Scott Patterson, Ph.D., Executive Director, Medical Sciences, Amgen Inc. |
| Keynote Presentation | |
| 12:35 | CASE STUDY: Application of Biomarkers for Early Decision Making and Patient Selection The application of biomarkers from FIH to late-stage development can enable better decisions to be made on the progression of candidate therapeutics. This can be achieved through analysis of direct effects of the candidates on biochemical pathways. Knowledge of the pathways that could influence response may also enable the development of patient stratification approaches. The application of these approaches and the range of different tools required will be presented. Scott Patterson, Ph.D., Executive Director, Medical Sciences, Amgen Inc. |
| 1:20 | CASE STUDY: Genetic and Functional Genomic Biomarker Discovery using Massively Parallel Sequencing Technologies Massively parallel sequencing technologies generate millions of shotgun, clonal tags per sample. We developed a pipeline for discovery of genetic and functional genomic biomarkers using massively parallel sequencing. Tag enumeration approaches appear to have significantly greater sensitivity and precision than array hybridization. Examples will be presented that demonstrate the promise of this approach for diagnostic discovery. Stephen Kingsmore, Ph.D., CEO, National Center for Genome Resources |
| 1:50 | Decyphering the Human Disease Proteome: Colon Cancer and Beyond The discovery of novel colorectal biomarkers for early diagnosis, therapy selection, and response monitoring are critical tasks. We will show how mass spectrometric approaches can be used to discover new biomarkers from primary surgical human tissue specimens. We will demonstrate how pre-fractionation methods such as heparin affinity enrichment enable significantly enhanced coverage of the low-abundance tissue proteome. Michael H. A. Roehrl, MD, Ph.D., Professor, Pathology and Laboratory Medicine, Massachusetts General Hospital, Harvard Medical School |
| Technology Workshop | |
| 2:20 | Enabling Robust Whole-genome Expression Profiling In Formalin-fixed, Paraffin-embedded (Ffpe) Cancer Tissue Samples
Formalin-fixed archival tissues represent an invaluable resource for cancer research. The ability to perform gene expression analysis in these samples will enable both prospective and retrospective studies, and should greatly facilitate research in correlating expression profiles with clinical outcomes. We have developed the DASL® Assay, for whole-genome expression profiling in FFPE samples; highly reproducible expression profiles (R2 >0.98) were generated with as little as 50 ng total RNA input (Am J Pathol. 2004 Nov; 165(5):1799-1807).Jian-Bing Fan, Ph.D., Illumina, Inc. |
| 3:00 | Networking Coffee Break |
| miRNA Biomarkers | |
| 3:30 | Chairperson's Remarks Mahendra Rao, MD, Ph.D., Vice President, Research, Stem Cells and Regenerative Medicine, Invitrogen Corporation |
| Keynote Presentation | |
| 3:35 | miRNA Expression in Stem Cells miRNA species have been shown to play an important role in the propagation and differentiation of adult and embryonic stem cell populations. Strategies for assessing miRNA and present some results on examining miRNA expression in embryonic and mesenchymal stem cells will be discussed. Methods of verifying expression and perturbation strategies will also be discussed. Mahendra Rao, MD, Ph.D., Vice President, Research, Stem Cells and Regenerative Medicine, Invitrogen Corporation |
| 4:20 | Transitioning miRNA Assays from the Discovery Lab to the Clinical Lab Assay features are important when transitioning from the discovery lab to the clinical setting. This is particularly true for miRNA profiles. Parameters that must be assessed include analytical and clinical sensitivity, analytical and clinical specificity, analytical repeatability and analytical calibration of each component of the miRNA profiling assay. The number of miRNAs in the profile and the requirement for throughput are additional issues that will be discussed. Keld Sorensen, Ph.D., Director, R&D Bioscience Group, Luminex Corporation |
| 4:50 | CASE STUDY: A New Diagnostic Platform for Prediction of Drug Response based on a Tumor's microRNA Profile Increasing evidence suggests that microRNAs play a key role in the initiation and progression of cancer and may comprise a novel class of molecular biomarkers. We have analyzed colorectal cancer specimens previously tested in the clinically validated Extreme Drug Resistance assay. The microRNA expression patterns were assayed on an LNA (Locked Nucleic Acid) microarray. Our analysis enabled identification of tumors that were resistant to 5-FU, Oxaliplatin, or Irinotecan, based solely on the tumor cell's microRNA profiles. William Ricketts, Ph.D., Vice President, Research, Oncotech (Exiqon) |
| 5:20 | End of Day One |
|
Main Conference - Day Two Tuesday, October 21, 2008 | PRE-CONFERENCE WORKSHOPS | DAY ONE | DAY TWO | DAY THREE | | |
| Sequencing and Detection Technologies | |
| Genomic Variation | |
| 8:00 | Chairperson's Remarks Dietrich Stephan, Ph.D., Co-founder and CSO, Navigenics, Director & Senior Investigator, Neurogenomics Division, Translational Genomics Research Institute |
| Keynote Presentation | |
| 8:05 | Assessing Genetic Risk Factors for Common Human Diseases Common diseases have both an environmental and a genetic component. We understand the major environmental exposures that predispose one to disease and have an established public health messaging vehicle surrounding exposure mitigation. No such ability or infrastructure has previously existed to test for and communicate the unique portfolio of genetic risk factors that we each carry. Genetic risk factor knowledge can be used to prevent or delay onset of disease. Dietrich Stephan, Ph.D., Co-founder and CSO, Navigenics, Director & Senior Investigator, Neurogenomics Division, Translational Genomics Research Institute |
| 8:50 | Frequency of Mitochondrial Polymorphisms in an Adult Cystic Fibrosis Population In adult cystic fibrosis (CF) patient populations, gram-negative bacteria, particularly Pseudomonas aeruginosa, frequently require aggressive therapy including systemic antibiotics, bronchodilators and airway clearance techniques. Aminoglycosides are frequently used to control these chronic airway infections. However they cause important nephro- and ototoxic effects. We investigated the genetic predisposition to aminoglycoside ototoxicity in a North American CF population by screening for polymorphisms in mitochondrial DNA sequences using DNA sequencing and microarray based approaches. Gary Hardiman, Ph.D., Assistant Professor & Director, BIOGEM, University of California at San Diego |
| 9:20 | Genetic Analysis of Cardiovascular Biomarkers and Disease Outcomes: Results from the Women's Genome Health Study Microarray technologies enable genomewide association studies of unprecedented scale, but the scientific merit of such studies also depends heavily on depth and accuracy of phenotyping. WGHS involves genome-wide SNP analysis of 27,939 women with 13+ years of incident disease data plus extensive biochemical phenotyping. WGHS reveals complex genetic architecture underlying surrogate biomarkers like CRP and LDL-C, and shows how genetics impacts their usefulness in predicting disease risk and treatment response. Alex Parker, Ph.D., Director, Molecular Sciences, Amgen Inc. |
| 9:50 | Networking Coffee Break, Exhibit and Poster Viewing |
| Next Generation Sequencing | |
| 10:30 | Deep Sequencing of a Tumor Transcriptome using the New Generation Sequencing Technologies Transcriptome analyses have been used extensively in genetic studies of cancer cells. The emergence of the new sequencing technologies allowed us to deeply explore the transcriptome of the breast tumor cell line HCC1954. With this level of transcriptome coverage, a variety of genetic and epigenetic events, including somatic mutations, chromosome breakpoints, splicing variants and genes differentially expressed were identified. Sandro de Souza, Ph.D., Director, Computational Biology, Ludwig Institute for Cancer Research, Brazil |
| 11:00 | A Mixed Application Next-Gen Sequencing Facility We describe a production mixed application next-gen DNA sequencing facility. In support of this facility we have developed and incorporated a LIMS and custom automation solutions in support of library production and template preparation. In addition we describe methods for template capture, whole transcriptome sequencing, and ultra high-throughput mutation detection. David J. Munroe, Ph.D., Advanced Technology Program, SAIC-Frederick, Inc. |
| Technology Workshop | |
| 11:30 | Using the Illumina Genome Analyzer to Study Gene Expression and Regulation
The Illumina Genome Analyzer is a high throughput DNA sequencing platform that routinely generates several billion bases of high quality sequence information from a single run. We will show examples of how the instrument is being used for a large variety of gene expression and gene regulation applications including mRNA-Seq, small RNA discovery, ChIP-Seq and DNA methylation analysis. Gary P. Schroth, Ph.D., Senior Director, Expression Applications R&D, Illumina Inc. |
| 12:00 | Networking Luncheon, Exhibit and Poster Viewing |
| Exhibit Hall Presentation | |
| 12:45-1:15 | Fluorous Immobilization for Microarray Formation 
Marvin S. Yu, Ph.D., Vice President of Technology, Fluorous Technologies, Inc. |
| Next Generation Sequencing (continued) | |
| 1:25 | Chairperson's Remarks Kun Zhang, Ph.D., Assistant Professor, Bioengineering, University of California at San Diego |
| 1:30 | Partitioning and Sequencing of the Human Genome and Methylome DNA sequencing technology has become a major driving force for genomic analyses. We have developed a versatile method for specific capture of any subset of genomic, transcriptomic and methylomic targets for next-generation DNA sequencing. Our method is based on large-scale production of DNA probes from programmable microarrays, and massive parallel capture of DNA targets with padlock probes. Some applications to the analysis of cancer and stem cells will be presented. Kun Zhang, Ph.D., Assistant Professor, Bioengineering, University of California at San Diego |
| 2:00 | Mapping Chromatin Structure and Nucleosome Fluctuation by Massive Parallel Sequencing: A Genomic-based Approach to Understand the Malaria Parasite Infection Cycle In recent years, genome sequences and high throughput technologies such as microarray platforms have marked a significant breakthrough in the understanding of the malaria parasite biology. However, to identify new antimalarial strategies, we must gain a comprehensive understanding of the parasites complex life cycle regulation. Using a genomic-base approach and massive parallel sequencing technology, we are aiming to understand the role of nucleosome occupancy in the transcriptional control of the parasite infection cycle. Karine G. Le Roch, Ph.D., Assistant Professor, University of California at Riverside |
| 2:30 | Networking Coffee Break, Exhibit and Poster Viewing |
| Technology Workshop | |
| 3:15 |
Complex variant detection in HIV and HLA with GS-FLX sequencing
Ultra Deep sequencing using the Genome Sequencer FLX platform provides a sensitive, high-throughput method for minor variant discovery in rapidly evolving viruses. Data will be presented on minor variant discovery in baseline HIV samples from the CPCRA FIRST clinical study. The long, clonal reads are also ideal for HLA haplotype determination since entire exons can be sequenced with no phase ambiguities, and the utility of GS-FLX Titanium chemistry for HLA haplotyping will be presented.Birgitte Binderup Simen, M.Sc., Ph.D., Group Leader, 454 Sequencing, Roche, Inc. |
| Next Generation Sequencing (continued) | |
| 3:55 | Chairperson's Remarks Jonathan Rothberg, Ph.D., Founder and former President/CEO, Curagen; Chairman, 454, Inc.; Chairman and Co-founder, RainDance Technologies |
| 4:00 | Honey Bees, Neanderthals, Transplant Patients, Genome Complexity, and Personal Genomes: The Creation and Future of Next Generation Sequencing Moore's law allowed 40 years of predictability in microelectronics. Moving sequencing to a chip, not through the miniaturization of Sanger sequencing, but by solid-phase massively-parallel sequencing has profoundly changed life science research. 454-Sequencing by being first to eliminate bacterial cloning, first to sequence in the miniature under flow conditions, and first to market, set the technology blueprint enabling this revolution and created the field of "next-gen" sequencing. What's next? Jonathan Rothberg, Ph.D., Founder and former President/CEO, Curagen; Chairman, 454, Inc.; Chairman and Co-founder, RainDance Technologies |
| 4:30 | Massively Parallel Resequencing from the Protein Coding Genome Next-generation DNA sequencing platforms have reduced the cost of DNA sequencing by over two orders of magnitude. We are developing methods to enable the cost-effective, targeted resequencing of the protein-coding fraction (~1%) of the human genome. Rare, nonsynonymous variation in the human genome may be a significant contributor to the genetic basis of common disease. These methods may also have relevance for the identification of somatic mutations in cancer. Jay Shendure, MD, Ph.D., Assistant Professor, Department of Genome Sciences, University of Washington |
| 5:00 | Next Generation Sequencing - Comprehensive Methods for Data Analysis Next generation sequencing data is exploited with carefully considered, efficient data mining strategies. Methods for transcriptome sequencing and ChIP-Seq analysis will be presented, demonstrating the possibilities for extending genome annotation, including biological implications of downstream analysis of enriched regions from ChIP-Seq data. Finally, we will discuss epigenetic modification data and meta-analysis possibilities by data consolidation on a whole genome scale. Martin Seifert, Ph.D., Vice President, Business Development/Collaborative Services, Genomatix Software, Inc. |
| 5:20 | End of Day Two Sessions |
| Molecular Diagnostics | |
| Global Molecular Diagnostics | |
| 8:00 | Chairperson's Remarks Bob Matson, Ph.D., FACB, Senior Scientist, Beckman Coulter |
| Keynote Presentation | |
| 8:05 | CASE STUDY: Democratizing Molecular Diagnostics: the Challenge of Implementing New Technology PCR and other nucleic acid amplification methods can potentially provide accurate and rapid,results for the management of infectious diseases in high-burden countries, but they require a high degree of technical sophistication, dedicated space, and specially trained staff. They are also designed to be run in batches for the sake of efficiency, but this negatively affects turnaround time medical impact. The GeneXpert MDR TB test will be described as a potential solution to a nearly intractable problem. David Persing, MD, Ph.D., Executive Vice President, Chief Medical and Technology Officer, Cepheid |
| 8:50 | Title TBA Abstract to come. Michael McKenna, Ph.D., CSO, Tethys Biosciences |
| 9:20 | Panel Discussion David Persing, MD, Ph.D., Executive Vice President, Chief Medical and Technology Officer, Cepheid Michael McKenna, Ph.D., CSO, Tethys Biosciences |
| 9:50 | Networking Coffee Break, Exhibit and Poster Viewing |
| Molecular Diagnostics for Infectious Diseases | |
| Keynote Presentation | |
| 10:30 | Chips, SNPs, and Microbial Attribution Each year nearly 76 million people fall ill to foodborne disease in the United States, resulting in approximately 325,000 hospitalizations, 5,000 deaths, and societal costs of at least 3.6x1011 dollars. Surveillance, monitoring of disease outbreaks, and prompt identification of the microbe involved are key to ensuring a safe food supply. We explore here how 'omics' technologies are being used to probe the pangenomes of foodborne pathogens to permit proper attribution. Eugene LeClerc, Ph.D., Director, Division of Molecular Biology, Center for Food Safety and Applied Nutrition, US Food and Drug Administration |
| 11:00 | Simultaneous Detection and Definitive Identification of Respiratory Pathogens Using Resequencing Microarrays TessArae's Resequencing Pathogen Microarray simultaneously detects and identifies hundreds of strains of viral and bacterial pathogens. Clinical studies of more than 800 respiratory specimens demonstrated superior sensitivity and specificity, with zero false positives, as compared to a combination of microbial culture and PCR testing. RPM provides single-specimen, single-test, same-day detection, identification and multi-gene sequencing results for real-time global epidemiology. Matthew Lorence, Ph.D., MBA, Vice President, Marketing and Sales, TessArae, LLC |
| 11:30 | Technology Workshop To learn more about sponsoring a Technology Workshop, please contact Sherry Johnson at (508) 614-1451 or sjohnson@ibcusa.com |
| 12:00 | Networking Luncheon, Exhibit and Poster Viewing |
| Exhibit Hall Presentation | |
| 12:45-1:15 | Fluorous Immobilization for Microarray Formation
Marvin S. Yu, Ph.D., Vice President of Technology, Fluorous Technologies, Inc. |
| Novel Microarray Applications in Molecular Diagnostics | |
| 1:25 | Novel Ultra-Sensitive Direct-Detection DNA Platform Using Metalized-DNA A new ultra-sensitive direct-detection DNA platform technology is described that eliminates the need for target amplification. Metalized-DNA (M-DNA) is a new confirmation of DNA wherein certain metal ions under strict reaction conditions can intercalate into the backbone of B-DNA forming a highly conductive molecule. Differential measurement of conductivity pre and post metallization provides the basis for the ultra-sensitivity. V. Randy White, Ph.D., CEO, Adnavance Technologies |
| 2:00 | 2007 Tech Idol Winner Cancer DSA™ - Disease Focused Microarrays Optimized for Use with FFPE Tissue This presentation covers the rationale and development of a range of custom gene expression microarrays designed to better reflect the complexity a variety of human disease transcriptomes. Examples will be shown of the application of these tools in biomarker discovery and validation from both fresh frozen and formalin fixed and paraffin embedded (FFPE) samples in breast, lung and colorectal cancer. Austin Tanney, Ph.D., DSA Programme Manager, Almac Diagnostics |
| 2:30 | Networking Coffee Break, Exhibit and Poster Viewing |
| 3:15 | Technology Workshop To learn more about sponsoring a Technology Workshop, please contact Sherry Johnson at (508) 614-1451 or sjohnson@ibcusa.com |
| Strategies for Synchronizing Companion Diagnostics Development with Drug Development | |
| 3:55 | Chairperson's Remarks Glenn A. Miller, Ph.D., Vice President and General Manager, Genzyme Analytical Services |
| 4:00 | Companion Diagnostics from the Clinical Lab Perspective The promise of better healthcare tailored to the individual places pressure on the companion diagnostic used for the identification of the appropriate drug/patient combination. The development of such companion diagnostics is not the traditional role of the pharmaceutical industry and has resulted in areas of confusion and concern. The effective development of companion diagnostics will take the close cooperation of the pharmaceutical, device and laboratory industries. Glenn A. Miller, Ph.D., Vice President and General Manager, Genzyme Analytical Services |
| 4:30 | Co-Development of Companion Diagnostics and Therapeutics: Diagnostic Developer Perspective While there is much excitement and enthusiasm around the development of predictive companion diagnostic biomarkers that will accompany molecularly targeted therapies in clinical practice, significant scientific, logistic, regulatory and health-economic challenges exist for all key stakeholders. These issues and thoughts on potential solutions will be presented from the perspective of a diagnostic developer. Eric Walk, MD, Senior Vice President & Chief Medical Officer, Ventana Medical Systems |
| 5:00 | Rx/Dx Roundtable Discussion Moderator: Glenn A. Miller, Ph.D., Vice President and General Manager, Genzyme Analytical Services Panelists: Eric Walk, MD, Senior Vice President & Chief Medical Officer, Ventana Medical Systems Mickey Williams, Ph.D., Director, Pharmacogenomics, Roche Molecular Systems William Ricketts, Ph.D., Vice President, Research, Oncotech (Exiqon) |
| 5:20 | End of Day Two Sessions |
| Biomarkers | |
| Integrating Systems Biology into Biomarker Discovery | |
| 8:00 | Chairperson's Remarks Bernhard Palsson, Ph.D., Galetti Professor of Bioengineering and Adjunct Professor Medicine, University of California at San Diego |
| Keynote Presentation | |
| 8:05 | Global Reconstruction of the Human Metabolic Network based on Genomic and Bibliomic Data The global human metabolic network, based on genome annotation Build 35 and comprehensive evaluation of >50 years legacy data, was manually reconstructed. The reconstruction process and how the resulting genome-scale network can be used for discovery of missing information, for the formulation of an in silico model, and as a structured context for analyzing high-throughput biological data sets will be discussed. Analysis of network structure indicates intracellular compartmentalization and potential use of correlated reaction sets for alternative drug target identification. Integrated analysis of high-throughput data sets with reconstruction enabled a global assessment of functional metabolic states. Bernhard Palsson, Ph.D., Galetti Professor of Bioengineering and Adjunct Professor Medicine, University of California at San Diego |
| 8:50 | New Ventures Enabling Biomarker-Guided Medicine Advances in systems biology measurements and models are enabling the development of new diagnostic approaches. This presentation will describe the work of several start-up companies each engaged in a different aspect of this field. Cases range from novel protein and metabolite-based multiplex markers, phosphorylation based functional diagnostics, single molecule analysis of DNA and Proteins, and molecular imaging. The commercial applications of these novel diagnostics include companion tests, prognostics, treatment monitoring as well as screening tests. Noubar Afeyan, Ph.D., Managing Partner and CEO, Flagship Ventures |
| 9:20 | The Functional Organization of the Brain Transcriptome We have used microarrays to explore human brain function, the emergence of higher cognition, and its relationship to disease. Using whole genome network co-expression analysis (WCGNA), we have developed a coherent framework that does not depend on a priori assumptions about gene function to provide a more holistic view of the transcriptome. These results underscore the power of network theory for contextualizing gene-expression data and demonstrate a previously undescribed structure to the human brain transcriptome. Daniel Geschwind, MD, Ph.D., Principal Investigator, Neurogenetics, UCLA |
| 9:50 | Networking Coffee Break, Exhibit and Poster Viewing |
| Imaging Biomarkers | |
| 10:30 | Radiogenomics: Bridging Conventional Diagnostic Imaging with Molecular Diagnostics Information embedded in the images obtained with existing non-invasive medical imaging tools such as CAT scans or MRI efficiently encode the global molecular activity of human cancers, thus in practice enabling one to visualize activity in the human genome. Thus, genomic activity of human tissues can be decoded by existing medical imaging tools, thereby enabling non-invasive, serial, and frequent molecular profiling for personalized medicine. Michael D. Kuo, MD, Assistant Professor of Radiology, Director Translational Medical Systems Laboratory, University of California at San Diego Medical School |
| 11:00 | Molecular Imaging of Signaling pathways in Cancer Molecular imaging aids in noninvasive characterization and quantification of biological processes in cell culture and live animals. We have recently developed novel molecular imaging tools for monitoring kinases and proteases which allow real time, dynamic and quantitative imaging of these enzymes. The impact of these technologies in oncological research for the process of drug discovery and preclinical determination of optimal drug dosage and schedule will be presented. Mahaveer S Bhojani, Ph.D., Assistant Professor, Center for Molecular Imaging, Department of Radiation Oncology, University of Michigan |
| Technology Workshop | |
| 11:30 | Ovation® Automation Solutions: Streamlining the target preparation workflow for expression biomarker discovery using limited, high value clinical samples
Advances in gene expression technologies and target preparation chemistries are driving efforts to increase throughput and sensitivity in biomarker discovery studies. Robust and reliable sample processing has therefore become critical for small, compromised RNA samples such as those from LCM, FFPE, whole blood, and biopsies. Workflows utilizing NuGEN target preparation methods on a variety of automation platforms will be described including a complete tissue to target workflow for FFPE samples on the Biomek® ArrayPlex.Joe Don Heath, Ph.D., Senior Director, Technical Marketing and Automation Solutions, NuGEN Inc. |
| 12:00 | Networking Luncheon, Exhibit and Poster Viewing |
| Exhibit Hall Presentation | |
| 12:45-1:15 | Fluorous Immobilization for Microarray Formation
Marvin S. Yu, Ph.D., Vice President of Technology, Fluorous Technologies, Inc. |
| Functional Analysis of Potential Biomarkers | |
| 1:25 | Chairperson's Remarks George A Calin, MD, Ph.D., Associate Professor, Experimental Therapeutics & Cancer Genetics, UT MD Anderson |
| 1:30 | Non-Coding RNA Principles in Medical Practice MicroRNAs were linked to the progression of all types of human tumors that were investigated to date. The main molecular alterations are represented by variations in gene expression, usually mild and with consequences for a vast number of target protein coding genes. These discoveries could be exploited for the development of useful markers for diagnosis and prognosis, as well as for the development of new RNA-based cancer therapies. George A Calin, MD, Ph.D., Associate Professor, Experimental Therapeutics & Cancer Genetics, UT MD Anderson |
| 2:00 | The Role of the let-7 MicroRNA Family During Development and Disease MicroRNAs regulate important developmental events in animals and are closely correlated with cancer. The let-7 miRNA family is postulated to function as tumor suppressor genes in a variety of human tissues, particularly in the lung, by regulating the oncogenes RAS, MYC, and HMGA2 as well as several cell cycle progression genes. We are investigating the role of let-7 during development and cancer, and on using miRNAs to suppress tumorigenesis. Aurora Esquela-Kerscher, Ph.D., Assistant Professor, Microbiology and Molecular Cell Biology, Eastern Virginia Medical School |
| 2:30 | Networking Coffee Break, Exhibit and Poster Viewing |
| Technology Workshop | |
| 3:15 | A Custom LIMS System for High Throughput Transcript Profiling
High throughput transcript profiling methodologies offer great promise for the discovery of gene signatures associated with disease progression and clinical outcome. We will review strategies for integrating automated RNA extraction from PaxGene-stabilized whole blood suitable for expression profiling using Affymetrix Genechip arrays. With an emphasis on tracking and handling data via a customized LIMS system, laboratories providing transcript profiling for biomarker discovery and diagnostic development efforts will find this data of interest.Norm Allaire, Ph.D., Senior Associate Scientist, Molecular profiling group, Biogen Idec Inc. |
| Metabolomic Biomarkers | |
| 3:55 | Chairperson's Remarks Kumar Sharma, MD, FAHA, Professor of Medicine, Director, Translational Research in Kidney Disease, University of California at San Diego/VA Medical System |
| 4:00 | Metabolomics in Clinical Trials of Novel Therapeutics To enhance the personalized approach to developing new therapies for common diseases we have developed a metabolomics biomarker platform to identify patients with high likelihood of responding to therapies. Using a non-targeted ESI-MS/MS approach to analyze urine metabolomics, bioinformatics and advanced visual intelligence software we will be able to identify metabolomic profiles associated with varying clinical outcomes. Metabolomics will enhance the clinical development of new therapies and allow for personalized approaches. Kumar Sharma, MD, FAHA, Professor of Medicine, Director, Translational Research in Kidney Disease, University of California at San Diego/VA Medical System |
| 4:30 | Metabolomics of Mice and Men: From Profiling to Diagnosis and Prognosis? Metabolite profiling of blood serum samples offers significant potential for improved diagnosis, prognosis and treatment follow-up. Using a targeted profiling NMR approach, we have studied several mouse models of human disease as well as numerous patient samples. With the aid of advanced statistical analyses, we can identify groups of metabolites that vary significantly with disease. Such 'biomarker profiles' are useful for monitoring the course of disease and treatment. Hans Vogel, Ph.D., Professor and AHFMR Scientist, Director, BioNMR Ce Biological Sciences, University of Calgary |
| 5:00 | Global Metabolomics: Navigating from Methods to Biology Human diseases manifest in complex downstream effects, affecting multiple biochemical pathways. We use a non-targeted, mass-spectrometry approach to metabolomics to investigate disease. Plasma from patients with inborn errors of metabolism were investigated for validation, and identified additional biomarkers. Investigating the microbiome interaction with the host revealed a surprisingly large effect on plasma biochemistry, and a drug-like response. The neurochemical effect of SIV-induced encephalitis was examined in rhesus macaques, addressing problems in central nervous system biochemistry and neurodegenerative diseases. Bill Wikoff, Ph.D., Director, Scripps Center for Mass Spectometry, Scripps Research Institute |
| 5:20 | End of Day Two Sessions |
| Plenary Keynote Address - Exhibit Hall | |
| 5:30 | Learning design principles from noisy small gene regulatory networks Modification and manipulation of biological networks requires an understanding of the underlying design principles. A complimentary approach to studying data derived interactions in large scale systems is based on the analysis of how molecular details influence the properties of small genetic network. On the molecular level, gene regulation is the outcome of protein and nucleic acid interactions. The relatively small molecule concentrations and intrinsic randomness of chemical reactions are only some of the sources of noise in gene regulation. Maximizing the information that the output protein of a pathway has about the input in the presence of molecular noise can lead to an understanding of the design principles of regulatory systems. I will discuss examples of how molecular noise can influence the cell's phenotype and lead to predict not only the connectivity but also the detailed biochemistry of a biological network. Aleksandra Walczak, Ph.D., Center for Theoretical Science, Princeton University |
| 6:15 | Networking Cocktail Reception in Exhibit and Poster Hall/Poster Competition Winner Announcement |
|
Main Conference - Day Three Wednesday, October 22, 2008 | PRE-CONFERENCE WORKSHOPS | DAY ONE | DAY TWO | DAY THREE | | |
| Sequencing and Detection Technologies | |
| Molecular Diagnostics | |
| Commercialization of Microarrays for Diagnostic and Personalized Genetics Applications | |
| 8:00 | Chairperson's Remarks Matthew Lorence, Ph.D., MBA, Vice President, Marketing and Sales, TessArae, LLC |
| 8:05 | Impact of DNA Microarrays on Molecular Diagnostics DNA microarrays are a powerful molecular diagnostic tool that facilitates multiplex, simultaneous analysis of tens to hundreds of markers that guide the identification of disease and its management. DNA microarrays have begun to move into mainstream clinical diagnostics. This presentation will review application areas of microarrays in molecular diagnostics, the market size, future growth prospects, key growth drivers, barriers, and other market forces such as regulatory and reimbursement challenges. Harry Glorikian, Managing Partner, Scientia Advisors |
| 8:15 | Investing in Technology to Drive Molecular Diagnostics The molecular diagnostics industry is being driven by the availability of sensitive, high-throughput detection methodologies for genome-wide analysis of DNA, RNA, protein and metabolites. This presentation will focus on how investment firms such as MDV make investments in tools and molecular diagnostics that drive personalized medicine. Examples from portfolio companies such as Pacific Biosciences and Raindance Technologies will be discussed. Rowan Chapman, Ph.D., Partner, Mohr-Davidov Ventures (MDV) |
| 8:25 | Legal, Regulatory and Political Issues Impacting the Use of Microarrays in the Age of Personalized Medicine The next generation of microarray technology is running headlong into the last generation of a legal and regulatory structure that struggles to keep pace with scientific change. Meanwhile, political and economic realities dictate that Congress and the new President attempt a drastic overhaul of health care in 2009, an undertaking that will have significant consequences in how microarrays can be a clinically and economically viable offering in the age of Personalized Medicine. Robert Wells, Partner, HEALTHfutures |
| 8:45 | Case Study: Pathwork® Tissue of Origin Test Commercialization Strategy - From CLIA test to Kit Commercialization of a molecular diagnostic test can take several forms as there are multiple pathways to the clinic. Pathwork Diagnostics, which is commercializing molecular diagnostics for oncology, recently launched a CLIA-certified Laboratory-based Pathwork® Tissue of Origin (TOO) Test that is used as an aid in the diagnosis of tissue of origin. The test utilizes a Pathchip™ microarray that is manufactured by Affymetrix and runs on the Affymetrix Genechip® platform. The next step is to work with the FDA to obtain clearance for a diagnostic kit version of the test. The strategies employed during this multi-step process will be discussed. David Craford, Vice President, Pathwork Dx |
| 9:05 | Panel Discussion
Matthew Lorence, Ph.D., MBA, Vice President, Marketing and Sales, TessArae, LLC Harry Glorikian, Managing Partner, Scientia Advisors Rowan Chapman, Ph.D., Partner, Mohr-Davidov Ventures (MDV) Robert Wells, Partner, HEALTHfutures David Craford, Vice President, Pathwork Dx |
| 9:35 | Networking Coffee Break, Exhibit and Poster Viewing |
| Biomarkers | |
| Proteomic Biomarkers | |
| 8:00 | Chairperson's Remarks David Wong, Ph.D., Professor, Dentistry, UCLA |
| 8:05 | Salivary Biomarkers for Clinical Applications Saliva is an emerging biofluid that is primed for translational and clinical applications. Fundamental to this effort is the recent development of two diagnostic alphabets in saliva (proteome and transcriptome) as well as point of care technologies that are poised to utilize validated salivary biomarker panels for robust clinical applications. David Wong, Ph.D., Professor, Dentistry, UCLA |
| 8:35 | Coupling Laser Capture Microdissection and Proteomics: From Protein Biomarkers to Molecular Imaging of Diseased Brain Methods for coupling laser capture microdissection of specific tissues in the brain with proteomic analyses and subsequent validation of identified biomarkers in animal models of disease will be presented. Development of targeted molecular imaging approaches against identified biomarkers for in vivo detecting and monitoring of brain diseases, such as stroke and brain tumors will also be discussed. Danica Stanimirovic, MD, Ph.D., Director, NeuroBiology Program, Institute for Biological Screening, National Research Councils |
| 9:05 | Qualitative and Quantitative Proteomic Reproducibility In order to identify and quantify protein biomarkers, results must be consistent between instruments and across laboratories. A proteomic sample should yield the same results from different mass spectrometers. A data independent acquisition method with a stringent protein identification protocol has the best chance of generating reproducible results from proteomic samples. In this study, results from samples run on various instruments will be compared to assess qualitative and quantitative reproducibility. Martha Stapels, Ph.D., Senior Research Chemist, Waters Corporation |
| 9:35 | Networking Coffee Break, Exhibit and Poster Viewing |
| Sequencing and Detection Technologies | |
| Technology Standards | |
| 10:30 | The NIST-ERCC Reference Material:Standard External Controls for Gene Expression Assays NIST and the External RNA Control Consortium (ERCC) have developed a standard set of sequences to use as "spike-in" controls for assessing the technical performance of gene expression assays. These sequences have been validated through a collaborative study, and will be made available as a reference material from NIST. Results from the collaborative study and a description of the reference material will be presented with potential applications and analysis. Shawn Baker, Ph.D., Senior Product Manager, Gene Expression, Illumina, Inc. |
| 11:00 | MAQC-II: Development and Validation of Class Prediction Models from Gene Expression Profiles The objective of the second phase of the Microarray Quality Control consortium (MAQC-II) is to characterize approaches for development and validation of classifiers using DNA microarray data for the purpose of class prediction studies. A standard operating procedure was developed to furnish a guideline for methodologies in classifier development and validation to assist analytical groups in preparing analysis protocols. Components of the SOP and issues regarding complexity, parsimony and multiplicity at the level of model selection will be discussed. Tim Davison, B. Math, Ph.D., Senior Scientist & Manager: Bioinformatics & Statistics, Asuragen, Inc. |
| Technology Workshop | |
| 11:30 | The SOLiD System - Setting New Standards in Genomic Analysis
The SOLiD™ System generates in excess of 6Gb of mate paired sequence data from a single run and recent throughput in the range of 12-17Gb has been demonstrated in Applied Biosystems R&D labs as well as customer sites. This enables the rapid sequencing of entire human genomes. As a result of this data availability, Applied Biosystems has sequenced a single Yoruban and analyzed the data for SNPs, insertions and deletions and structural variations. This presentation will review some of the challenges of analyzing such data sets. The advantages of base encoding will be discussed, especially in context of SNP calling. In addition, the use of Mate pairs and the latest tools for utilizing SOLiD™ System data will be presented.Michael Rhodes, Ph.D., Senior Application Manager, High Through-put Discovery, Applied Biosystems |
| 12:10 | Networking Luncheon, Exhibit and Poster Viewing |
| Emerging Technologies | |
| 1:25 | Chairperson's Remarks Winston Patrick Kuo, DDS, MS, DMSc, Director, Laboratory for Innovative Translational Technologies, Harvard School of Dental Medicine |
| 1:30 | Digital Gene Expression Analysis Rapid digital gene expression analysis for high density multiplexed characterization and transcript qualification was used in studies at the Oncogenomics Core facility of the University of Miami, Sylvester Comprehensive Cancer Center. Data generated with this novel enzyme-free alternative to microarray and PCR-based approach will be presented. Toumy Guettouche, Ph.D., Associate Scientist, University of Miami, Miller School of Medicine |
| 2:00 | Targeted Extraction of Specific Non-Contiguous Loci of Mouse Chromosome 1 for Next Generation Sequencing using HybSelect To maximize the power of next generation sequencing, an efficient method of separating chromosomal DNA from sequences of interest is required to reduce sample complexity. We will demonstrate enrichment and recovery 100 non-contiguous loci of mouse chromosome 1 using HybSelect. HybSelect employs Geniom® Biochips containing arrays of target-specific capture probes that, in combination with integrated microfluidics, enable automated hybridization and elution of sequences. Markus Beier, Ph.D., Vice President Application Development, febit AG |
| 2:30 | Networking Coffee Break, Exhibit and Poster Viewing |
| Novel Technologies and Arrays | |
| 3:00 | Chairperson's Remarks Neil Winegarden, Ph.D., Director, Microarray Centre, United Health Network |
| 3:05 | A Novel, Scalable Liquid Array Platform for Molecular Analysis We are developing a cost-effective and flexible multiplexed quantitative assay system that merges the advantages of fixed 2D arrays (e.g. microarrays) with liquid arrays (e.g. microbeads) using Encoded Sortable Particles (ESPs). ESPs are 60x75x3 micron, photolithographically-manufactured, optically-encoded particles that can be orientationally-controlled and arrayed in an ordered manner on a 2D surface using magnetic force. These ESPs are being used to develop an Arrayable Liquid Array platform. Chris Herold, Ph.D., MBA, CFO & Vice President, R&D, Arrayomics Inc. |
| 3:30 | Single Molecule Detection for Molecular Diagnostics and Individualized Testing Metal enhanced fluorophore-linked nanoparticles allow detection of proteins, post-translational modifications and single copies of genes without amplification. Enhanced sensitivity at the single molecule level, with no nucleic acids/protein extraction and amplification requirement, can reduce costs and enable automation. Detection of multiple pathogens or targets of interest can be multiplexed. Quantification and localization of chemokine receptor CCR5 on the cell surface of T-lymphocytes with respect to individual's susceptibility to HIV-1 infection with this assay will be presented. Richard Y. Zhao, MS, Ph.D., Associate Professor Pathology, Microbiology-Immunology and Human Virology, Division Head MolecularPathology, Director Molecular Diagnostics Lab, UMD Medical Center |
| 4:00 | End of Conference |
| Molecular Diagnostics | |
| Biomarkers | |
| Pathways to Biomarker and Diagnostics Reimbursement | |
| 10:30 | Overview Biomarkers are poised to redefine many aspects of health care practice and policy. More than virtually any other factor, reimbursement will play a pivotal role in the success of biomarker-based technologies and personalized medicine approaches. This session will explore current practice and policy issues related to reimbursement of biomarkers, including:
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| 11:00 | CASE STUDY: Payor Perspective: Analytical and Clinical Metrics used in the Health Technology Assessment Process The revolution of lower-cost molecular biology means that today, very sophisticated biomarker-based tests reach the clinical marketplace with substantial validation data within a few years of discovery. This session will evaluate diagnostics reimbursement from the payer perspective and discuss challenges that are faced when molecular innovation outruns legacy coding, coverage and payment systems for diagnostics reimbursement and how to work toward a winning strategy despite market uncertainties. Bruce Quinn, MD, Ph.D., Senior Health Policy Specialist, Foley Hoag, LLC |
| 11:30 | Diagnostics Industry Perspective: Planning for Reimbursement There is a significant need educate payers and other health decision makers on the value of appropriate coverage and reimbursement of molecular diagnostics. A fully integrated personalized medicine paradigm will be driven by the ability to eliminate the reimbursement and coverage barriers that impact a patient's ability to access technological innovations in biomarker-based tests. This session will explore the challenges of obtaining appropriate reimbursement from the perspective of the diagnostics manufacturer and offer suggestions for overcoming obstacles to reimbursement. John R. Ridge, National Director, Managed Care and Reimbursement, diaDexus, Inc. |
| 12:00 | Networking Luncheon, Exhibit and Poster Viewing |
| 1:25 | Venture Capitalist Perspectives on Investment in Biomarker-based Technologies: How Important is Reimbursement Potential? Abstract to come. Joseph Ferrara, Executive Vice President, Boston Healthcare Associates Inc. |
| 2:00 | Panel Discussion Eric Faulkner, Ph.D., MPH, Director of US Reimbursement and Market Access, RTI Health Solutions John R. Ridge, National Director, Managed Care and Reimbursement, diaDexus, Inc. Bruce Quinn, MD, Ph.D., Senior Health Policy Specialist, Foley Hoag, LLC Joseph Ferrara, Executive Vice President, Boston Healthcare Associates Inc. |
| 2:30 | Networking Coffee Break, Exhibit and Poster Viewing |
| Molecular Diagnostics | |
| Molecular Diagnostics Nearing the Clinic | |
| 3:00 | Chairperson's Remarks Ho-Sheng Lin, MD, FACS, Associate Professor, Department of Otolaryngology-Head and Neck Surgery, Wayne State University School of Medicine |
| 3:05 | SEPT9: A DNA Methylation-based Early Detection Biomarker for Colorectal Cancer Through DNA methylation marker discovery and characterization a particularly robust methylation marker, SEPT9, was found to be present in greater than 90% of colorectal cancer (CRC) tissues. A real-time PCR assay amplifying methylated SEPT9 DNA found in the blood of individuals with CRC has been validated as an effective plasma biomarker for CRC detection in several large case control studies and is now in development as an in vitro diagnostic. Catherine Lofton-Day, Ph.D., Vice President, Molecular Biology, Diagnostics, Epigenomics Inc. |
| 3:30 | On-Chip Diagnostic Immunoassays of Tumor Specific Autoantibodies for the Early Detection of Cancer The humoral immune response is an exquisite biosensor of antigens expressed by tumor cells. A multianalyte immunoassay, based on a panel of tumor antigens recognized by the immune biosensor, could provide sufficient sensitivity and specificity for early cancer detection. Using a high-throughput approach combining phage-display technology, protein microarrays-based serological profiling, and bioinformatics tools, a panel of diagnostic tumor antigens has been identified. There are numerous advantages to employing serum antibodies as the analytes, not the least of which is the ability to readily adapt these assays to standard clinical platforms. Ho-Sheng Lin, MD, FACS, Associate Professor, Department of Otolaryngology-Head and Neck Surgery, Wayne State University School of Medicine |
| 4:00 | End of Conference |
| Biomarkers | |
| Extending RNAi into Therapeutics | |
| 3:00 | Chairperson's Remarks Andreas G. Bader, Ph.D., Senior Scientist, Mirna Therapeutics, Inc. |
| 3:05 | miRNA Replacement Therapy for Cancer MicroRNAs (miRNAs) are small, naturally occurring molecules that function as gatekeepers of the genome, regulating multiple gene products and coordinating multiple cellular pathways. miRNAs play a critical role in the development of human disease and therefore can be exploited for therapeutic intervention. We have validated the concept of "miRNA Replacement Therapy" which involves introducing synthetic miRNAs into diseased tissues in an effort to reactivate pathways that drive a therapeutic response. Examples of miRNA therapeutics in mouse models of cancer will be presented. Andreas G. Bader, Ph.D., Senior Scientist, Mirna Therapeutics, Inc. |
| 3:30 | CASE STUDY: Multi-Targeted siRNA Cocktail for Novel Cancer Therapeutics Using siRNA cocktails to silence multiple disease genes is truly realizing the advantages of siRNA therapeutics. We have developed a set of siRNA cocktails using our proprietary algorithm and "Tri-Blocker" platform. Those siRNA cocktails were validated in mouse xenograft models of breast carcinoma, glioblastoma, melanoma and prostate adenocarcinoma, for their therapeutic potential using polymeric and liposomal carriers. Combining siRNA cocktails with monoclonal antibody in the same regimen further improved treatment. Patrick Y. Lu, Ph.D., President & CEO, Sirnaomics, Inc. |
| 4:00 | End of Conference |
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