4:00 pm Event Chairperson’s Opening Remarks
Cindy Crowninshield, Conference Director, Cambridge Healthtech Institute

4:15 Informatics: Integration & Convergence
John Reynders, Ph.D.,Vice President & Chief Information Officer, Johnson & Johnson, Pharma R&D

5:00 Welcome Reception in the Exhibit Hall
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7:30 am Registration and Morning Coffee

8:15 Event Chairperson’s Opening Remarks
Phillips Kuhl, Co-founder and President, Cambridge Healthtech Institute 

8:20 Drug Development: Evolving Challenges and Opportunities
Joshua Boger, Ph.D., President & Chief Executive Officer, Vertex Pharmaceuticals, Inc.

9:00 Keynote Presentation & 2008 Benjamin Franklin Award
Robert Gentleman, Ph.D., Head of Program in Computational Biology, Fred Hutchinson Cancer Research Center

9:30 Coffee Break, Exhibit and Poster Viewing in the Exhibit Hall

10:50 Track Chairperson’s Remarks
Jean-Jacques Codani, Founder and Chief Scientific Officer, GenomeQuest, Inc.

11:00 Towards Personal Genomics - Tools for Navigating the Human Reference Genome 
The Human Reference Genome, published in September 2007 by the J. Craig Venter Institute, is the first high-quality diploid genome of a human. We will describe the web based analysis tools developed for navigating the diploid reference genome, and look forward to an era where hundreds of individual human genome sequences will be available.
Saul Kravitz, Ph.D., Director, Software Engineering, J. Craig Venter Institute

11:30 pm Use of Genomics as a Tool to Identify Stage-Appropriate Therapeutic Intervention Strategies
Genomic patterns have the potential to reveal the progression of host responses during illness and help to pin-point early indicators of tissue involvement or organ failure. In combination with limited proteomics, these find-ings can be used to identify markers that will permit therapeutic efforts to be focused to divert impending serious outcomes. Our studies using a systems approach to integrate clinical, physiological, -omics and mathematical modeling have revealed stages of illness progression during which time certain standard therapies may no longer be effective, yet they also reveal other therapeutic strategies. The aim is to identify sets of biomarkers that could be rapidly determined for near-real-time assessment of patient status.
Marti Jett, Ph.D., Chief, Department of Molecular Pathology, Walter Reed Army Institute of Research

12:00 Next Generation Sequencing: A Solution in Search of a Problem?
40 years after the first DNA sequencing in 1968, we appear to be on the verge of profound changes in sequenc-ing technology that increase the efficiency (throughput and cost) of DNA sequencing dramatically. Indeed the throughput is reaching levels such that harnessing the data generated by the next generation technologies is a non-trivial informatics problem. We will discuss the problems which can be solved with high speed sequencing. Even simple analysis of this torrent of data requires sophisticated computational platforms and high throughput analysis workflows. Without such informatics support, next generation sequencing may not be a solution looking for a problem but rather a partial solution.
Kamalakar Gulukota, Senior Director, Content Development, GenomeQuest, Inc.

1:45 Linking Genetic Epistasis and Genomic Pathways to Complex Health Outcomes 
Evaluating the complex health outcomes of common diseases and identifying the genetic and genomic factors that determine effectiveness and risks of a drug for a particular patient or group of patients is crucial to guide de-velopment, assist with dosing, and avoid disproportionate restrictions or even unwarranted withdrawal. Many of the statistical methods currently used, however, are based on the (generalized) linear model and, thus, not well suited to comprehensively analyze data with different, non-linear scales (binary, ordinal, and quantitative). The talk will explore how new statistical approaches, enabled by novel informatics tools, facilitate innovative uses of personalized medicine. 
Knut Wittkowski, Ph.D., D.Sc., Director, Biostatistics, Epidemiology, and Research Design, Center for Clinical and Translational Science, The Rockefeller University

2:45 Microarrays: Bench-to-Bedside
Functional genomics and proteomics approaches have rapidly evolved over the last years and have provided the basis for groundbreaking discoveries in basic and clinical research. As the technologies become more mature and validated, bench-to-bedside clinical applications rapidly emerge. Our focus has been to identify gene signatures in patients with various types of cancer for early detection, cancer progression, metastasis, survival as well as re-sistance or sensitivity to therapy. We have developed novel bioinformatics approaches for biomarker discovery and individualized gene expression analysis that are enhancing the identification of aberrant signaling pathways in individual patients and clinical application of microarray data for patient stratification and management. Exam-ples of microarray and bioinformatics approaches and their potential clinical applications in renal, prostate and breast cancer will be presented together with the implementation of the new fully automatized Affymetrix plat-form for high-throughput 96 well microarray analysis.
Towia Libermann, Ph.D., Associate Professor of Medicine, Beth Israel Deaconess Medical Center

3:15 Refreshment Break, Exhibit and Dedicated Poster Viewing

3:45 Pathways to Targets: Qualitative Reasoning and Quantitative Modeling
Much of the complexity in biology exists within the dynamic nature of its pathways and processes. To improve the ability to identify and validate biomarkers for use as diagnostics and potential therapeutic targets, it is critical to be able to handle incomplete information about coordinated molecular interactions in a manner that supports rational experimental design and the integration of experimental data with literature data into operational mod-els. We have been using both Petri nets and Stochastic Activity networks to evaluate the use of Herceptin in breast disease and to model the impact of SNP’s on developmental processes that can stratify individual patient’s risk for disease, e.g. breast and ovarian cancer, osteoporosis, cardiovascular disease. Both the methods and the results will be presented.
Michael Liebman, Ph.D., Executive Director, Windber Research Institute

4:15 Institution-Wide Copy Number Variation Analysis and Reporting Systems 
Array CGH and SNP arrays become widely accepted for diagnostics of many diseases and for development of per-sonalized medicine. Availability of terabytes of public array CGH datasets outside institutions and accumulation of proprietary Copy Number Variation (CNV) data inside institutions calls for efficient and robust IT systems to man-age and analyze the data. We would like to highlight major challenges in analyzing CNV profiles in the framework of very large high-resolution datasets and in presence of various biological factors. We would like to demonstrate our approach to solving such problems as cross-platform array data compatibility, seamless integration with pub-licly available data sources (GEO, ArrayExpress etc), data management for accumulated CNV and expression pro-files and data fusion for very large aberration datasets.
Anton Petrov, Ph.D., Director, Cytogenetics, infoQuant, Ltd.

4:45 Protein Microarrays and Quantum Dot-Probes for Cancer Biomarkers Early Detection 
This talk will describe a novel approach for detection of cancer markers using Quantum Dot Protein Microarrays. Quantum dots and protein microarrays are relatively new technologies that offer very unique features that to-gether allow detection of cancer markers in biological specimens at picogram/ml concentrations. 
Tatyana Zhukov, Ph.D., Assistant Professor, Cancer Prevention and Control Division, H. Lee Moffitt Cancer Center & Research Institute

5:15-6:15 2008 Best of Show Awards/Reception in the Exhibit Hall

6:15 Exhibit Hall Closes 

7:00 2008 Bio-IT World’s Best Practices Awards/Dinner

7:30 am Registration and Morning Coffee

8:00 Event Chairperson’s Opening Remarks
Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World 

Keynote Introduction: 
Ron Ranauro, President and CEO, GenomeQuest, Inc. 

8:05 Personalized Genetics: Advancements & Driving Change
Linda Avey, co-Founder, 23andMe, Inc.

8:45 The Future of Personal Genomics George Church, Ph.D., Professor of Genetics and Director of the Center for Computational Genetics, Harvard Medical School Dietrich Stephan, Ph.D., Co-founder and Chief Science Officer, Navigenics, Inc. Jeffrey M. Drazen, M.D., Editor-in-Chief, New England Journal of Medicine; Distinguished Parker B. Francis Professor of Medicine, Harvard Medical School Fred D. Ledley, MD, Professor and Chair, Bentley College; Founder and Chairman, My Genome John Halamka, MD, MS, CIO, Harvard MedicalSchool Linda Avey, co-Founder, 23andMe, Inc.

9:45 Coffee Break, Exhibit Viewing, Vendor Theater Presentations, and Poster Competition in the Exhibit Hall
Informatics for Biomarkers

10:45 Track Chairperson’s Remarks

11:00 An Integrated Framework for Multiple Myeloma Research
Joint with Track 3
The Computational Biology and Functional Genomics Laboratory at the Dana Farber Cancer Institute, in collabo-ration with InforSense, is developing a novel web-based application to support Multiple Myeloma research. The application provides research scientists an integrated view of clinical and laboratory data that allows them to better understand the relationships that exist. Scientists can identify the mechanisms that can be linked to poor response to chemotherapy and use that information to develop new therapeutics. This application supports a range of research activities performed by various users, including study designers, biologists, statisticians and software developers. Its functionality allows researchers to utilize features that support their specific needs: Study designers can check participant metrics and sample availability, biologists can access statistician data and link to public-domain data sources, statisticians can export formatted data sets, and developers can rapidly de-velop and deploy new applications to accommodate evolving research needs. In this talk, we will cover the spe-cifics of the application, as well as the ROI that has been achieved in terms of both cost and science. 
John Quackenbush, Ph.D., Professor of Biostatistics and Computational Biology, Dana-Farber Cancer Institute

11:30 Understanding Biology: Multi-Modal Correlation Networks for Biomarker Discovery and Qualification 
The project involved a multi-party collaboration including federal, corporate biotechnology and informatics soft-ware institutions applying biotechnology and information technology to data integration, process management and biomarker activity modeling for diagnostics. This talk will demonstrate how 
semantic network tools can be successfully applied to complex multi-modal data environments to qualify and validate biomarkers and to gain insights on biological
functions which can be used in modeling system’s processes more accurately. 
Alan Higgins, Ph.D., Vice President, Preclinical Development, Viamet Pharmaceuticals

12:00 pm Towards Quantitative Metabolomics
Metabolomics is an emerging field of ‘omics’ research that is concerned with the high-throughput characterization and comparison of the small molecule metabolites in the metabolome. Traditionally, metabolomics researchers have used chemometric, statistical and pattern recognition techniques to characterize metabolic variation, with-out much of a focus on metabolite quantification and identification. In this presentation I will describe some of the emerging techniques (in NMR, LC-MS and GC-MS) and newly developed database resources that are allowing metabolomics researchers to systematically identify and quantify large numbers of metabolites. This “quantita-tive” approach to metabolomics not only complements traditional methods, but it should open the door to identi-fying many new disease biomarkers.
David Wishart, Ph.D., Professor of Computing Science and Biological Sciences, University of Alberta

12:30 Luncheon in the Exhibit Hall

2:00 Exhibit Hall Closes

2:00 Evaluating Genomic Response of Xenografts to DNA Interference (DNAi®) Treatments 
This discussion provides key insights into the development of an emerging DNA-based potential oncology treat-ment regime utilizing therapeutic oligonucleotides, leveraging widely-available bio-IT tools and technologies. Methods and technologies for the use of gene expression profiling to identify the molecular impact of DNAi thera-pies on human Prostate cancer xenografts will be discussed. This case study outlines how potential biomarkers for assessing DNAi therapy efficacy in future preclinical and clinical studies, as well as how data illuminating a specific DNAi drug’s mechanism of action was generated. Given enormous recent interest in RNAi-based potential therapeutics, this talk will discuss and contrast the DNAi approach.
Richard Gill, Ph.D., President and Chief Executive Officer, ProNAi Therapeutics, Inc.

2:30 Rapid RNAi Informatics Development with PointDragon^TM 
The ability to rapidly implement and evolve laboratory workflows in an environment of changing platform tech-nologies is a constant challenge. We will show how at Sirna Therapeutics (a wholly owned subsidiary of Merck & Co., Inc.) we have addressed this using the PointDragon Platform to develop a custom LIMS implementation that integrates sample tracking and annotation, data translation and long-range planning and resource management in a single application. The system provides the flexibility to support Sirna’s discovery pipeline using standardized business rules for decision-making, while allowing ready access to underlying data for long-term process analysis. We will describe lessons learned and comparisons to our experience with other LIMS solutions.
Alex Birch, LIMS Developer, Sirna Therapeutics (a wholly owned subsidiary of Merck & Co., Inc.) 

3:00 Molecular Profiling of Clinical Stem Cell Products 
Production of adult stem cells for clinical use requires extensive safety testing, and demonstration that biological potency is retained over significant population doublings in expansion. We have utilized chromosomal SNP analy-sis to augment karyotypic stability measurements, and transcriptional profiling and gene methylation analysis to demonstrate equivalency of early and late expansion products. Use of differential profiling strategies has allowed discovery of novel marker sets which distinguish primitive from more mature adult stem cell types.
Robert Deans, Senior Vice President, Regenerative Medicine, Athersys, Inc.

4:00 Conference Adjourns