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7:00 am Conference Registration
7:30 Breakfast Presentation (Sponsorship Opportunity)
8:15 – 9:15 “Java and Jive” Discussion Groups
Grab a cup of coffee and join a facilitated discussion group focused around specific scientific and technology related topics. This unique session allows conference participants to exchange ideas, experiences, and develop future collaborations around a focused topic. Current discussion groups include:
TABLE 1: Cloud Computing in Bioinformatics
Host: David Dooling, Ph.D., Assistant Director, The Genome Center at Washington University in St. Louis
Discussion topics include:
• What is cloud computing and what are its advantages?
• What types of analysis are appropriate for cloud computing?
• How do I secure my data in the cloud?
TABLE 2: PCR-Based Technologies for Single Locus Methylation Studies
Host: Tomas K. Wojdacz, M.S., Ph.D., Institute of Human Genetics University of Aarhus, Denmark
Discussion topics include:
• How can I design my experiment?
• What are the most common mistakes in the experimental design?
TABLE 3: CNV in Evolution and Disease
Host: James R. Lupski, Ph.D., Professor and Vice Chair, Molecular & Human Genetics & Pediatrics, Baylor College of Medicine
Discussion topics include:
• New mutation rates for CNV
• Gene duplication/triplication
• Exon shuffling and CNV
TABLE 4: Advances in NGS Library Preparation
Host: Nicholas Caruccio, Ph.D., Director of Marketing Development, EPICENTRE Biotechnologies
Discussion topics include:
• Limiting and Challenging Samples
• Simplified Work Flow
• High Throughput Methods
• Assessing Library Quantity and Quality
TABLE 5: Transcriptome Alignment and Analysis
Hosts: Rick Nelson, Ph.D., Senior Next Generation Sequencing Software Engineer, DNASTAR; Tom Schwei, General Manager, DNASTAR
Discussion topics include:
• De novo assembly and mRNA discovery
• Expression and SNP analysis
• Transcript analysis of novel genomes
TABLE 6: Who Needs a Map?
Host: Harris Lewin, Ph.D., Professor of Immunogenetics, Animal Sciences, University of Illinois
Discussion topics include:
• Do current sequence-only strategies provide the necessary information to interpret cancer genomes?
• What are the prospects for closing the gaps in genome assemblies using next-generation sequencing data?
TABLE 7: Cloud Storage: Solving Performance and Scalability with Content Scale-Out
Host: Christopher Williams, Product Manager Storage and Software Products, DataDirect Networks
Discussion topics include:
• Global Content Data Storage Strategy: What can it do for your organization? Performance through simplicity
• Existing Technologies: Advantages and disadvantages of a public and private cloud.
TABLE 8: NGS and Medical Genomics: The Challenge of Making NGS Data Relevant to the Clinician
Host: Martin Siefert, Ph.D., Vice President of Marketing, Genomatix Software
Discussion topics include:
• Personalized and translational medicine: Is NGS the key to getting there?
• What are the challenges of correlating NGS data profiles with disease phenotype or drug efficacy?
• Do we have all of the pieces of the big picture: linking NGS platforms, data analysis, and phenotypic correlations to the practicing clinician?
TABLE 9: Multiple Mutations Characterize the Cancer Genome
Host: Lawrence Loeb, Ph.D., Professor & Director, Gottstein Memorial Lab & Pathology, University of Washington
Discussion topics include:
• Are single base substitutions the most frequent alterations?
• Are deletions important?
• Why are so few mutations found in DNA repair gene and DNA polymerases?
• What is significant about subclonal mutations in tumors?
• What are the consequences of tumor DNA heterogeneity?
• Does lethal mutagenesis have a place in HIV or cancer therapy?
TABLE 10: Whole Transcriptome Analysis Using Now-Generation Sequencing Technology
Host: Min Li, Ph.D., Field Application Specialist, Partek, Inc.
Discussion topics include:
• Differential expression and alternative splicing analysis of mRNA’s
• Differential expression of small RNA
• Coding SNPs discovery and allele expression analysis
• Other RNA sequencing applications
TABLE 11: Overcoming Obstacles That Hamper Epigenome Mapping in Clinical Samples
Host: Kenneth Nephew, Ph.D., Professor of Medical Sciences; Cellular and Integrative Physiology; Obstetrics and Gynecology; Co-Director, Center for Integrated Cancer Biology; Assistant Director, Basic Science Research, Indiana University Simon Cancer Center
Discussion topics include:
• Obstacle 1. Can methylation mapping techniques be used to analyze DNA from formalin-fixed, paraffin-embedded (FFPE) and plasma?
• Obstacle 2. Can we lower the input DNA requirements for genome wide analysis (large amount of genomic DNA are typically required)?
• Obstacle 3. Can we overcome incomplete bisulfite conversion, which can result in artifacts?
TABLE 12: The Potential of Epigenetic Modulators in Clinics
Host: Xian-Ping Lu, Ph.D., Chief Executive Officer & Chief Scientific Officer, ChipScreen Biosciences
Discussion topics include:
• What recent progress have we made in oncology?
• What other indications may be used for epigenetic modulation?
• What are some hurtles in disease treatment using epigenetic modulation?
TABLE 13: Removal of Contaminating DNA in qPCR and qRT-PCR
Host: Morten Elde, Ph.D., Head of Application Development, Biotech Marine Biochemicals
Discussion topics include:
• Carry-over prevention
• Removal of genomic DNA before RT-PCR
• Removal of contaminating DNA from reaction components
TABLE 14: Moving Beyond Single Genome Analysis
Host: Richard Resnick, Vice President, Software and Professional Services, GenomeQuest, Inc.
Discussion topics include:
• What questions can be asked of genome-wide or exome-wide variation across 1,000 samples? 100,000?
• What are the best-of-breed approaches for determining patterns of inheritance using NGS data?
• What are the hurdles to applying NGS multi-sample variation analysis to translational medicine?
• What are your plans with the 1,000 Genomes data?
TABLE 15: Epigenetic Changes in Cancer and Body Fluids
Host: Zdenko Herceg, Ph.D., Head of Epigenetics Group, International Agency for Research on Cancer (IARC)
Discussion topics include:
• Predictive value of epigenetic signatures (DNA methylation and microRNAs in cancer)
• Quantitative detection of DNA methylation changes in body fluids
• High-throughput and genome-wide analysis of epigenetic changes
TABLE 16: Large Scale Sequencing Centers, Specialized Service Providers, Your Personal Sequencer - Can These Efforts Be Organized?
Hosts: Didier G. Perez , Co-Founder and COO; Karen Roberts, Director of Sales; Eureka Genomics
Discussion topics include:
• What are the implications of the very large sequencing centers initially controlling the technology and grant monies?
• What are the advantages of “de-centralizing” these efforts?
• What part will Data Analysis and Bioinformatics play? Will data analysis keep up with sequencing capabilities? Gene Annotation?
• Are most labs currently equipped to provide this data analysis and bioinformatics?
• How will Specialized (outside) Services play a part in both NGS and Data Analysis efforts?
TABLE 17: What Single Molecule Sequencing Can Do for Your Research
Host: Patrice M. Milos, Ph.D., Vice President and Chief Scientific Officer, Helicos BioSciences Corporation
• Do you require genomic analyses with small sample quantities where bias can become more problematic?
• Would Direct RNA Sequencing meet a gap in your genomic studies?
• Is sample multiplexing a key need for your studies?
• Are your samples formalin-fixed parrafin-embedded and require different genomic solutions?
TABLE 18: The Future of qPCR – Adaptation to Meet New Demands
Host: Natasha Paul, Ph.D., Scientific Investigator, TriLink BioTechnologies, Inc.
Discussion topics include:
• Future advancements in qPCR – what will they be? (smaller volumes, faster cycling reagents and instruments, new detection methods, improvements in specificity)
• Personalized medicine – how can qPCR be made more robust for reliable diagnostic routine use?
• Next generation sequencing – how can qPCR adapt to support work in this growing field?
TABLE 19: Enabling World Class Research through Innovative Data Management Strategies
Host: Peter Brey, HP WW Storage Business Development Manager, Hewlett Packard
A Reality Check –What is the Real Cost of Sequencing?
Next-generation sequencing (NGS) has energized the scientific community and captured the public’s attention. As we move into the new era of genomic sequencing, it’s important to quantify these new technological advances and answer the question…. What is the return on investment? In this exciting Plenary Session, join genomic thought-leaders from diverse backgrounds as they share their views on when and where they believe NGS’ ROI will first be realized.
9:20 Chairperson’s Remarks
Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
9:25 Studies on Charcot-Marie-Tooth Disease: My Personal Genome Experience
James R. Lupski, Ph.D., Professor and Vice Chair, Molecular & Human Genetics & Pediatrics, Baylor College of Medicine
Whole genome sequencing (WGS) may revolutionize medical diagnostics through rapid identification of alleles that cause disease; however, even in cases with simple patterns of inheritance and unambiguous diagnoses, the relationship between disease phenotypes and their corresponding genetic changes can be complicated. Comprehensive diagnostic assays must therefore identify all possible DNA changes in each haplotype and determine which are responsible for the underlying disorder. To demonstrate the utility of human WGS for medical diagnosis, we identified a family with a recessive form of Charcot-Marie-Tooth (CMT) disease. We showed that separate sub-clinical phenotypes independently segregated with each of the two disease associated mutations. This presentation will explain how WGS can identify clinically relevant, medically actionable variants and provide diagnostic information for patient management.
10:05 Unlocking Genomic Medicine: Answering the Why
Mark P. Stevenson, Ph.D., President and COO, Life Technologies
Technology has come a long way from the days when it cost $3 billion and took 13 years to sequence a human genome. The rate of advancement suggests that sequencing costs will drop below the $1000 level in the next few years. Even today, a genome can be sequenced in a matter of weeks, making the issue of cost and time largely irrelevant, although accuracy remains critical. As more individuals have the ability to finance the sequencing of their genome, the question must become what one does with that information. While the scientific community has largely accepted the utility of sequencing for research purposes, the use of the technology in a clinical setting has yet to be fully addressed or accepted by the medical community. Sequencing can uniquely improve patients' lives in diseases such as cancer that are driven by biological pathways. Life Technologies is bridging the gap between research and medicine by forming collaborations that not only demonstrate the clinical utility of sequencing, but also pave the way for how this technology can potentially be used by a new class of physicians.
10:45 Networking Coffee Break, Exhibit & Poster Viewing
11:15 The Business of Genomics
G. Steven Burrill, Chief Executive Officer, Burrill & Company
As candidate drugs that were discovered as a result of mapping the human genome move to the clinic, genomics is proving itself. And now the second wave of genomics, proteomics, pharmacogenomics and systems biology is having a positive impact on the development of more targeted and personalized therapeutics and diagnostics, which in turn is leading to next generation medicines. This talk will examine how companies are harnessing the power of this revolutionary new knowledge to bring new products to market.
11:55 Panel Discussion with Plenary Keynote Speakers
Moderator: Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
12:15 pm Close of Morning Session
12:30 Luncheon Presentation 
NGS-level Sequence Data Management for Researchers, with a Complete, Cloud-enabled API for Developers
Richard Resnick, VP of Software and Professional Services, GenomeQuest
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Next-Generation Sequencing (NGS) is undoubtedly the “now-generation” -- alive, thriving, and driving discovery. As costs continue to fall and ease increases, these massively parallel, high-throughput sequencing platforms are infiltrating more and more aspects of biological research. This TECH EXPO showcases industry leaders as they present the latest technological attributes and biomedical applications of their sequencing platforms.
2:00 Chairperson's Remarks
Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
Sponsored by:
 2:05 Sponsored Presentation
Robert Nutter, Ph.D., Senior Specialist, Product Applications, Applied Biosystems
2:25 Sponsored PresentationSponsored by:
An Unbiased, Quantitative View of Genome Biology Possible Only with Helicos Single Molecule Sequencing
John F. Thompson, Ph.D., Senior Director, Genomic Research, Helicos Biosciences Corporation
Helicos Single Molecule Sequencing provides a unique view of genome biology through direct sequencing of cellular nucleic acids in an unbiased manner providing accurate, digital quantitation and sequence information. The simple sample preparation involves no ligation or PCR amplification, allowing direct sequencing of DNA or RNA molecules. With this simplicity comes the opportunity to measure genome biology in ways not previously possible. We will present results from the diversity of applications possible on the Helicos® Genetic Analysis System and discuss why issues of amplification and sequence bias matter in your everyday research efforts. Further we will demonstrate applications unique to the Helicos single molecule sequencing technology providing new capabilities that are unmet or underserved by amplification-based technologies. Those new applications include the direct sequencing of RNA, the unique ability to sequence ancient and degraded nucleic acids and the absolute quantitation of miRNAs,
DNA and RNA molecules.
3:05 Sponsored Presentation
Sponsored by:
 Changing the Trajectory of DNA Sequencing
Gary P. Schroth, Ph.D., Sr. Director, Illumina
The Illumina HiSeq2000 is a new high-throughput DNA sequencing platform that produces an unprecedented output of more than 1 billion reads and over 200 Gb of very high quality data per run. We have used the throughput of this instrument to complete human genome sequencing projects, whole genome methylation analysis in cancer/normal pairs, and complete transcriptome analysis of multiple human tissues. Each of these very large sequencing projects can now be done in a single instrument run using the HiSeq2000. In this presentation we will review the data from these projects, look in detail at the system performance for different applications, and discuss how this new
system enables massive new studies in genomics, gene expression and regulation.
3:35 Networking Refreshment Break, Exhibit & Poster Viewing
4:15 Sponsored Presentation
Sponsored by:
 Transforming Complete Human Genome Sequencing
Aaron Solomon, VP Sales and Business Development, Complete Genomics, Inc.
Complete Genomics provides high-throughput, affordable, and complete genome sequencing of human populations. Our goal is to enable commercial-scale research of the genetic mechanisms underlying complex diseases and drug responses, with a view to ensuring important advances in the diagnostic and therapeutic markets. Our complete human genome sequencing service presents human disease investigators with a turnkey solution for their human genome sequencing needs. We provide customers with research-ready reports including variant analysis and annotation data, and thus greatly accelerate their path to discovery.
4:45 Sponsored Presentation
Sponsored by:
 SPRIworks - A Simplified Sample Preparation System for Next Generation Sequencing
Patrick J. Finn, Ph.D., Director, Research and Development, Beckman Coulter Genomics
The emergence of second generation sequencing technologies from Roche/454, Illumina and Life Technologies has enabled scientists to generate vastly increased data sets from their sequencing experiments. The dramatic increase in throughput however is supported by workflows that are relatively complicated and labor intensive, requiring skilled labor and significant hands-on time to prepare samples for each instrument. At Beckman Coulter we have created a simplified automated workflow for the leading second generation sequencing platforms that utilizes the core SPRI™ magnetic particle to create an automated system for sample preparation.
5:15 Interactive Panel Discussion with Sequencing Leaders
Moderator: Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
As the genome unit price of NGS platforms continues to tumble, excitement is growing about the scientific and commercial potential of sequencing systems. This Interactive Panel Discussion continues the traditional “roast” by the moderator and panelists, while trading insights on the latest NGS scientific and technological advances. Full audience participation warmly encouraged!
5:45 -7:00 Welcoming Reception in Exhibit Hall
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