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IBC’s 2nd Annual

Next-Generation Sequencing & Genomic MedicineConcrete Applications for Research, Drug/Diagnostic Development and Patient Care

Discover novel uses for next-generation sequencing

to improve science and healthcare

Drug Discovery & Diagnostic Development WeekAugust 1-3, 2011 • Hyatt Regency San Francisco • San Francisco, CA

Bronze Sponsors:

Association Partner:

• The advent of mid-throughput sequencing (PGM, GS Junior, MiSeq)

• Fetal diagnostics and clinical diagnostic applications

• Sequencing of viral and bacterial populations

• Clinical applications in cancer, HLA and the immune repertoire

• Breakthroughs in single molecule sequencing

• Clinically-informed cancer genomics research

Keynote Speakers:

Richard L. Schilsky, M.D. University of Chicago

Leroy Hood, M.D., Ph.D.Institute for Systems Biology

Paul S. Meltzer, M.D., Ph.D. National Cancer Institute

Markus Warmuth, M.D. Novartis

Stephen H. Friend, M.D., Ph.D. Sage Bionetworks

Matthew K. Waldor, M.D., Ph.D. Harvard Medical School

Charles R. Cantor, Ph.D. Sequenom

IBC’s 8th InternationalNext-Generation Molecular DiagnosticsIBC’s 5th Annual Empowered Antibody TherapiesIBC’s 5th Annual New Frontiers in CancerIBC’s Inaugural Targeted Therapeutics

Co-located with:

Register early for best rates at 1-800-390-4078 • Use Priority Code D11203LRIG www.drugdisc.com

Event-at-a-Glance: Drug Discovery & Diagnostic Development WeekMonday, August 1 Tuesday, August 2 Wednesday, August 3

Next-Generation Sequencing & Genomic MedicineNext-Generation Molecular DiagnosticsEmpowered Antibody Therapies

New Frontiers in Cancer

Targeted Therapeutics

Scientific Advisory BoardChristopher Carlson, Ph.D., Assistant Member, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center Henry Erlich, Ph.D., Vice President, Discovery Research and Director of Human Genetics, Roche Molecular SystemsStephen H. Friend, M.D. Ph.D., President, Co-Founder and Director, Sage Bionetworks Stefanie S. Jeffrey, M.D., Chief Surgical Oncology Research, Stanford University School of Medicine Hanlee P. Ji, M.D., Assistant Professor, Oncology, Stanford University School of Medicine and Senior Associate Director, Stanford Genome Technology Center

Paul Kayne, Ph.D., Senior Principal Scientist, Applied Genomics and Genomic Technologies, Bristol-Myers SquibbPatrice Milos, Ph.D., Vice President and CSO, Helicos Bioscience Mostafa Ronaghi, Ph.D., Senior Vice President and Chief Technology Officer, Illumina, Inc.Michael Rhodes, Ph.D., Senior Manager, Sequencing Portfolio, Applied Biosystems, part of Life Technologies Timothy J. Triche, M.D., Ph.D., Director Center for Personalized Medicine, Children’s Hospital Los Angeles; Professor and Vice-Chair, USC Keck School of Medicine

Next-Generation Sequencing & Genomic Medicine Advances in next-generation sequencing and genomic technologies are unlocking the biology of disease in ways not previously possible, leading to a paradigm change in target finding, drug development and patient treatment. The mission of this unique conference is to explore in one forum the most exciting, current examples of next-generation sequencing being APPLIED in research, drug/diagnostic development and patient care. Register now and gain access to emerging, unpublished data and ground-breaking applications from scientists on the leading-edge of this exciting field.

IBC’s 8th International

Next-Generation Molecular DiagnosticsMulti-Gene Assays and Diagnostics Using Genomics, Proteomics and Next-Generation Sequencing to Improve Clinical-Decision Making and Drug Development

• Multivariate diagnostics linking disease biology and clinical data• Proteomics-based high-value diagnostics• Gene expression/genotyping and genomics-based diagnostics• Molecular diagnostics enabled by next-generation sequencing• Companion diagnostics: the drug-diagnostic “value” paradigm

For full conference agenda, abstracts, and speaker information, visit www.IBCLifeSciences.com/MDx

IBC’s 5th Annual

Empowered Antibody Therapies

IBC’s 5th Annual

New Frontiers in Cancer

IBC’s Inaugural

Targeted TherapeuticsAntibody-Drug Conjugates, Bispecifics and Enhanced Antibodies

• Antibody-drug conjugates in the clinic• Bispecifics empowering the immune system• Multifunctional targeting• Payload delivery and tumor-targeting strategies• Antibody-cytokine and fusion molecules

For full conference agenda, abstracts, and speaker information, visit www.IBCLifeSciences.com/Antibody

Targeted Medicine, Individualized Treatment and Clinically-Informed Drug and Diagnostic Development

• Clinically-informed cancer genomics research• Characterization of rare, circulating tumor cells• Translational and individualized cancer medicine• Antibody-drug conjugates for cancer• Bispecific antibodies and multifunctional targeting

For full conference agenda, abstracts, and speaker information, visit www.IBCLifeSciences.com/Cancer

Drug Conjugates, Nanoparticles, and Localized Therapeutics• Targeted nanocarriers and nanoparticles • Overcoming resistance to targeted drugs• Antibody-drug conjugates in the clinic• Bispecific antibodies and multifunctional targeting• Tissue-specific delivery, payloads and BBB traversal

For full conference agenda, abstracts, and speaker information, visit www.IBCLifeSciences.com/Targeted

Your registration allows access to these co-located conferences:

Translate Clinically-Informed Research into Improved HealthcareBiology-Driven Science • Predictive Medicine • Novel Therapies

2 To Register, Call: (800) 390-4078 • Fax: (941) 365-0104 • E-mail: [email protected] • Use Priority Code D11203LRIG

7:45 Registration and Coffee

8:50 Chairperson’s Welcome and Opening RemarksStefanie S. Jeffrey, M.D., Chief Surgical Oncology Research, Stanford University School of Medicine

Sequencing of HLA and the Immune Receptor Repertoire 9:00 Immune Monitoring by High-throughput Sequencing

High-throughput DNA sequencing of rearranged immune receptor loci enables global characterization of human immune responses and lymphoid malignancies. Applications of human immunoglobulin heavy chain (IGH) sequencing include detection of minimal residual lymphoma/leukemia following treatment, tracking the peripheral blood B cells responding to vaccination, and monitoring autoimmune diseases.Scott D. Boyd, M.D., Ph.D., Assistant Professor of Pathology, Stanford University

9:30 TCRB and IgH Repertoire Profiling Using High Throughput SequencingThe adaptive immune system is relevant to many disease states including autoimmune disease, infections, and cancer. At the core of the adaptive immune system is the diversity of T cell receptors (TCR) and B cell receptors (BCR) allowing the recognition of previously experienced or new antigens. We have been obtaining immune receptor repertoire profiles using high throughput sequencing technology of amplified TCRB and/or IgH from blood or other samples. These profiles can be utilized in the elucidation of many disease states.Malek Faham, M.D., Ph.D., Chief Scientific Officer, Sequenta, Inc.

10:00 Exploring Signatures of Pathogen Exposure in the Adaptive Immune RepertoireThe adaptive immune system expands cells carrying pathogen-specific antigen receptors as part of the immune response to pathogenic exposures. The breadth of antigen receptors involved in the response to any specific pathogen is finite, and generally oligoclonal. Recent work in our group has identified a significant overlap in the realized antigen-receptor repertoire, and we will describe our efforts to screen for shared pathogen-specific sequences across individuals with shared exposure histories.Christopher Carlson, Ph.D., Assistant Member, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center

10:30 Networking Refreshment Break

11:00 High Resolution, High Throughput HLA Class I and Class II Typing Using Next-Generation Sequencing The HLA loci are the most polymorphic genes in the human genome; distinguishing the thousands of HLA alleles is challenging. The amplification of HLA class I and class II exons with 454 fusion primers containing MID tags and the 454 adaptors followed by clonal sequencing of the amplicons on the GS FLX and the benchtop GS Junior systems allows high resolution, high throughput HLA typing. The Conexio ATF 454 software assigns genotypes by comparing the sorted sequences to the IMGT HLA sequence database. For very high throughput, we have used the Fluidigm Access Array instrument and the “4 primer” approach to achieve automated genomic PCRs with 48 different MID tags.Henry Erlich, Ph.D., Vice President, Discovery Research and Director of Human Genetics, Roche Molecular Systems

11:30 Human Antibody Diversity: From Libraries to Humans and BackNGS of human antibody phage display libraries gives insights to human immune repertoire, and sequencing of human immune repertoire helps in antibody library design. This reiterative process opens the door to understand the relationship between human antibody repertoire and disease.Jaume Pons, Ph.D., Chief Scientific Officer, Pfizer Rinat

12:00 Immune Sequencing in Diagnostic and Therapeutic ApplicationsWe are developing technologies and analytical tools to leverage the information registered in the immune repertoire. We discuss time course tracking of immune responses in patients using flu vaccination as a model, as well as preliminary survey of the immune repertoire in rheumatoid arthritis and of HIV elite controller patients.Francois Vigneault, Ph.D., Postdoctoral Ragon Institute Fellow, George Church Laboratory, Harvard Medical School

12:30 Lunch on your own

1:40 Chairperson’s RemarksHenry Erlich, Ph.D., Vice President, Discovery Research and Director of Human Genetics, Roche Molecular Systems

Keynote Presentations: Molecular Diagnostics on the Cutting-Edge

1:45 Whole Genome-Based Molecular Epidemiology: The Origin of the Haitian Cholera Outbreak Strain

Cholera had not been present in Haiti for more than a century until the current outbreak began in October 2010. We used 3rd generation single molecule real time DNA sequencing to rapidly characterize the genomes of Haitian V. cholerae isolates as well strains from other parts of the globe. Our analyses showed that the Haitian cholera outbreak strain bears striking similarity to V. cholerae isolates from South Asia.Matthew K. Waldor, M.D., Ph.D., Howard Hughes Investigator, Edward H. Kass Professor of Medicine, Harvard Medical School

2:30 Non-Invasive Sequencing of Fetal DNA In an average pregnancy, 13% of the free DNA in the

peripheral circulation of the mother originates from the fetus. This is sufficient that non-invasive detection of fetal aneuploidies by DNA sequencing will soon become routine. It is also possible to reconstruct most of the fetal genome sequence by sampling the DNA in the mothers blood, but this is still too costly for routine use. The methods developed to analyze these mixed maternal fetal DNA samples should be applicable to other problems in DNA mixture sequencing.Charles R. Cantor, Ph.D., Chief Scientific Officer, Sequenom, Inc.

3:15 Networking Refreshment BreakMolecular Diagnostics Enabled by Next-Generation Sequencing

3:45 Noninvasive Prenatal Diagnostics with Next Generation Sequencing and Whole-Genome HaplotypingPrenatal diagnosis of genetic diseases currently requires invasive procedures. Cell-free fetal DNA in maternal plasma can serve as a noninvasive alternative to prenatal diagnosis. This presentation summarizes technological advances in the field of noninvasive prenatal diagnosis: the detection of fetal aneuploidy using next-generation sequencing, and the determination of fetal genotypes using a combination of sequencing and haplotyping techniques.H. Christina Fan, Ph.D., Postdoctoral Fellow, Laboratory of Steve Quake, Stanford University

Monday, August 1, 2011

3 Visit www.drugdisc.com for up-to-date information on this event • Use Priority Code D11203LRIG

Tuesday, August 2, 2011

Monday, August 1, 2011 (continued)

4:15 Diagnostic Applications of Single-Molecule, Real-Time (SMRT™) DNA Sequencing SMRT DNA Sequencing is a 3rd generation DNA sequencing technology that allows for the acquisition of DNA sequence information with long read lengths, fast time to results, and fine workflow granularity. Dr. Turner will discuss the power of SMRT sequencing for diagnostic applications, with examples that include sequencing of clinical samples containing mixed hepatitis C virus subtypes and comprehensive mitochondrial DNA sequencing from patients.Stephen W. Turner, Ph.D., Founder and Chief Technology Officer, Pacific Biosciences

4:45 Next-Gen Sequencing Transforms the Diagnosis of Mitochondrial DiseasesMitochondrial diseases are clinically very heterogeneous and are notoriously difficult to diagnose. The emerging consensus is that the frequency of mitochondrial diseases in childhood is 1:500, which is as high as all childhood cancers combined. The diagnosis of mitochondrial disease has depended predominantly on biochemical tests of moderate sensitivity and specificity.Steve S. Sommer, M.D., Ph.D., Founder and President, MEDomics LLC

5:15 Methylation-Based Biomarkers for Predictive and Prognostic Use MDxHealth’s proprietary Methylation-Specific PCR (MSP) platform identifies DNA methylation-based oncology biomarkers for theranostic applications, utilizing epigenetic sensitization in combination with different next–generation based sequencing approaches. A comprehensive epigenome-wide profiling pipeline has been established. This approach combines a sensitive and specific discovery phase with a smooth transition to analytically validated assays for clinical trial testing. We have been applying these approaches in high throughput mode on samples ranging from model systems like cell-lines and xenografts to primary patient material, in cancer-types ranging from colon, lung, prostate to bladder.Wim Van Criekinge, Ph.D., Vice President Science and Technology, MDxHealth, Belgium

5:45 Close of Day

8:10 Chairperson’s Remarks

Keynote Presentations: Individualizing Patient Care 8:15 Implementing Individualized Cancer Care

Individualizing cancer care has the potential to improve patient outcomes and reduce the cost of cancer treatment. As currently conceived, individualized cancer care relies on the use of biomarkers to refine prognosis, select optimal therapy, monitor the effects of treatment and prospectively identify patients at high risk of treatment toxicity. Implementation of these approaches requires high quality biospecimens, robust and analytically validated assays and physician education regarding the clinical interpretation and application of biomarker data. Also essential is a business and regulatory model that encourages clinical validation of potential biomarkers and supports adequate reimbursement for their use. These issues will be addressed with the use of contemporary examples.Richard L. Schilsky, M.D., Professor of Medicine; Chief, Section of Hematology-Oncology; Deputy Director, Comprehensive Cancer Center, University of Chicago and Past President of ASCO

9:00 P4 Medicine: Personalized, Predictive, Preventive and Participatory

This presentation will discuss the foundations of P4 medicine—the idea that medicine is an informational science; the systems or holistic approach to disease that will provide insights into disease mechanisms and new approaches to diagnosis and therapy; the emerging technologies that will open new dimensions of patient data space and the need for new analytic tools to handle the billions of data points that will surround as a virtual cloud each individual patient in just 10 years. It will also discuss the societal implications of P4 medicine as well as the need for strategic partnerships to realize the challenging opportunities of P4 medicine.Leroy Hood, M.D., Ph.D., President, Institute for Systems Biology

9:45 Networking Refreshment Break and Exhibit/Poster Viewing

10:25 Chairperson’s RemarksChristopher Carlson, Ph.D., Assistant Member, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center

Sequencing of Bacterial and Viral Populations: Implications for Drug & Diagnostic Development

10:30 Application of Ultra-Deep Sequencing Technologies to Detect Minority Drug-Resistant Viral Variants in HIV-Infected Patients: The Implication for Clinical CareRecent data has demonstrated that drug-resistant HIV variants that exist at very low levels within a viral population are clinically important as they can rapidly grow under drug selection pressure and lead to therapy failure. This presentation will discuss the clinical importance of minority resistant viral variants and how new ultra-deep sequencing technologies can be used to detect minority variants.Michael J. Kozal, M.D., Professor of Medicine, Yale University School of Medicine, Chief, Section of Infectious Diseases, VA CT Healthcare System

11:00 Clostridia That Inhabit the Human Gut: Who Are They, and How Much Can We Trust Them?The Clostridiales group is a numerically dominant component of the healthy human gut microbiota, which collectively conveys many health benefits, including helping us to extract calories and nutrients from our food, educating our immune system, and protecting us from pathogens. The Clostridiales group, however, also contains potent gut pathogens, such as Clostridium difficile, and an ill-defined collection of opportunistic pathogens that can infect blood and tissue or overgrow in the small intestine. In this work, I use information on the distribution of Clostridial species across healthy and sick individuals, to identify which Clostridial species are disease-associated. Comparing the genomes of commensal vs pathogenic types, and subsequent growth experiments, suggests that an increased tolerance to oxygen, which can be acquired by horizontally transferred genes, is associated with virulence. Catherine A. Lozupone, Ph.D., Postdoctoral Researcher, Laboratory of Rob Knight, University of Colorado


Tuesday, August 2, 2011 (continued)

Strategic Discussion ForumChallenges and Opportunities

for Next-Generation Sequencing Sample Preparation

Tuesday, August 2, 2011 • 11:30am-12:30pmThis informative panel discussion covering the important topic of sample preparation in next-generation sequencing will be hosted by the LRIG (Laboratory Robotics Interest Group) Bay Area Chapter. Access to this discussion is included in your conference registration.

Panel Moderator: Hosted by:

Michael Biros, Executive Chair, LRIG Bay Area

11:30 Ultrasensitive Detection of Rare Variants in Admixture Populations using Next-generation SequencingThe viral load of an infected individual often contains a population of quasi-species each with a different genome. A rare resistant variant may survive lethal selection and proliferate causing prolonged illness. We describe innovations to both statistical and experimental methodology using targeted next-generation sequencing to identify rare mutational events. We present results on detection of mutations present at a low-level 0.1% with high sensitivity (100%) and specificity (99%) using an experimentally defined admixed population of synthesized DNA. We apply our approach to clinical samples of H1N1 infections and identify mutations present in the sample at levels less than 1%.Patrick Flaherty, Ph.D., Postdoctoral Fellow, Biochemistry, Stanford University

12:00 Next-Generation Sequencing Assays for Clinical DiagnosticsPathogenica is developing next generation sequencing assays for clinical diagnostics, which will provide higher sensitivity and accuracy than existing nucleic acid tests, at a reduced cost. We will preview forthcoming clinical applications of next generation sequencing for viral genotyping, describe our DxSeq technology that significantly reduces the workflow from tissue sample to sequencing result, and report evaluation of our assays in clinical tissue samples.Graeme Doran, Ph.D., Chief Scientific Officer, Pathogenica, Inc.

12:30 Networking Luncheon and Exhibit/Poster Viewing 1:55 Chairperson’s Remarks

Paul Kayne, Ph.D., Senior Principal Scientist, Applied Genomics and Genomic Technologies, Bristol-Myers Squibb

Next-Generation Sequencing for Diverse Applications 2:00 Molecular Testing for 595 Severe Childhood Recessive

Diseases by Next-Generation SequencingWe have developed a next-generation sequencing based carrier screening and diagnostic test for 595 severe diseases with childhood onset, that meet ACMG guidelines for genetic testing for rare, highly-penetrant disorders. This test is being validated in a CLIA approved lab and will be available for physician ordering in Q3, 2011.Darrell L. Dinwiddie, Ph.D., Director of Lab Operations, Center for Pediatric Genomic Medicine, Children’s Mercy Hospital and Adjunct Professor, National Center for Genome Resources

2:30 Sponsored Presentation OpportunitySponsored presentations offer the opportunity for your company to present an exciting application of next-generation sequencing in this conference session. For more information, please contact Sherry Johnson at [email protected]

3:00 The Agilent Technologies SureSelect™ Platform for Target Enrichment: Focusing Next-Gen Sequencing on DNA That MattersThis presentation will discuss Agilent’s SureSelect Target Enrichment platform, its main applications and explore recent literature and scientific discoveries the technology has enabled. It will highlight the current SureSelect product portfolio, which extends from Human All Exon kits to small capture customizable assays, including updates on new, recently launched products. It will also discuss how to scale projects with automation and to study thousands of samples with SureSelect.Sheila Purim, Ph.D., Technical Applications Specialist, Agilent Technologies, Inc.


Media Partners

Association Partner:

Event Partner:

The Advent of Mid-Throughput/Lower-Cost Sequencers: Applications for Everyday Biological and Clinical Research

4:15 A Stream-lined Process for Amplicon Resequencing using Ion Torrent’s Personal Genome Machine Coupled with Fluidigm’s Access Array A multiplexed approach to sample processing is essential to maximize data return of a single run on a next-generation sequencing platform. Using Ion Torrent’s PGM, we have streamlined our follow-up validation studies for our exome and whole genome initiatives. The presentation will focus on the ability to process hundreds of suspected targets of interest across hundreds of samples during a single day. The ability to process hundreds of samples per day will undoubtedly lead to faster discovery of underlying genetic markers for many of today’s current diseases. Joe Boland, Development and Next-Generation Sequencing Operations Manager, National Cancer Institute

4:45 MiSeq Personal Sequencing SystemIllumina is introducing a low-cost personal sequencing system. The platform performs provides with read lengths of up to 2 x 150 base pairs. The utility of this device for targeted sequencing, Immuno Repertoire Profiling, small genome sequencing, ChIP-Seq, and RNA-Seq will be discussed.Mostafa Ronaghi, Ph.D., Senior Vice President and Chief Technology Officer, Illumina, Inc.

5:15 Replacing Sanger Sequencing with NGS: Sequencing of Full Length ClonesWe currently sequence a large number of full length clones to verify their sequence integrity after routine cloning operations. We typically “primer walk” or “shotgun” sequence these clones, with the method choice dependent on gene size. This is a time consuming and expensive process. Using smaller sized NGS instruments, and appropriate pooling and barcoding, we can now replace Sanger sequencing with faster and more cost effective methods.Paul Kayne, Ph.D., Senior Principal Scientist, Applied Genomics and Genomic Technologies, Bristol-Myers Squibb

5:45 Close of Day Two

Visit www.drugdisc.com for up-to-date information on this event • Use Priority Code D11203LRIG 5

Wednesday, August 3, 2011

11:10 Chairperson’s RemarksTimothy J. Triche, M.D., Ph.D., Director, Center for Personalized Medicine, Children’s Hospital Los Angeles; Professor & Vice Chair, USC Keck School of Medicine

Cancer Genomics: Clinical and Research Applications of Next-Generation Sequencing

11:15 Applying Clinical Genomics to Advance the Science of Medicine: Case Study of a Triple Negative Breast Cancer StudyThe potential value for NGS to revolutionize biomedical discovery research is clear, but the value for directly applying NGS in a clinical setting to improve health care delivery remains to be demonstrated. This presentation will share TGen’s experience in applying clinical NGS to individualize cancer treatments, with emphasis on a triple negative breast cancer study currently underway. The talk will also review the unique challenges and solutions for interpreting individual (n=1) genomes to recover clinically actionable knowledge that can be applied to improve patient care.Spyro Mousses, Ph.D., Vice President, Office for Innovation, Senior Investigator & Director, Center for BioIntelligence, TGen

11:45 Comprehensive Next-Generation Sequencing for Clinically Actionable Mutations from Routine Clinical SamplesWith the increasing availability of genomically targeted therapies, the comprehensive description of a patient’s specific tumor genome can be an effective diagnostic approach that informs plausible therapy selection to enable better treatment as well as enabling the detection of rare mutations that reveal innovative therapeutic strategies.Alexis Borisy, Chief Executive Officer, Foundation Medicine, Inc.

12:15 Human Disease Research and Drug Development in the Era of Next Generation SequencingIn this presentation, we discuss two complementary approaches to drug development made possible by NGS applications. In the first approach, multi-omic data sets provide the foundation for understanding a disease state’s biology. In the second, a focus on single data types (e.g., genomic) allows for the rapid determination of new drug targets. We present projects demonstrating BGI’s experience in supporting both approaches, including work that has informed drug development and advanced our understanding of complex diseases like cancer.Joyce Peng, Ph.D., Director, BGI Americas

12:45 Networking Luncheon and Exhibit/Poster Viewing 2:00 Therapeutic Targets from Cancer Sequencing Studies

Due to advances in next-generation sequencing technologies, whole-exome and whole-genome sequencing of human tumor DNA is now possible. However, it is not a simple task to decipher the biology that lies coded in the resulting lists of somatic mutations. We will discuss functional genomics approaches to identification of novel oncogenes and therapeutic targets from cancer sequencing data, and describe novel receptor tyrosine kinase targets uncovered by these approaches.Heidi Greulich, Ph.D., Instructor, Dana-Farber Cancer Institute and Visiting Scientist, The Broad Institute of MIT and Harvard

2:30 Streamlined Targeted Amplification for Next-Generation Sequencing Studies: Applications in Cancer GenomicsNext generation sequencing platforms have dramatically reduced sequencing costs. However, it currently remains too expensive to routinely resequence entire human genomes in order to discover genetic variants or somatic mutations underlying tumorigenesis. Therefore, a need exists for multiplexed, targeted amplification methods that allow for the analysis of multiple genomic regions in large cohorts. The novel microfluidic platform, the Access Array™ system enables just such research with minimal cost, time and sample material.Speaker to be announced, Fluidigm


8:00 – 8:30 Interactive Workshop Software Solutions for Sequencing Assembly and Analysis DNASTAR will demonstrate our next-generation sequence assembly and analysis software tools. We will show templated and de novo sequence assembly, SNP detection, RNA-Seq and ChIP-Seq. DNASTAR’s software assembles a whole human genome in < 24 hours on a desktop computer. We’ll assemble several genomes during the workshop and analyze results from numerous assembly projects. One attendee will win an iPad!Matthew Keyser, Next-Gen Application Scientist, DNASTAR

8:45 Chairperson’s Remarks

Keynote Presentations: Clinically-Informed Genomics and Drug Development

8:50 Bringing Genomics to the Oncology Clinic: Opportunities and Challenges Because the intrinsic biology of each patient's tumor plays a major role in governing the response to therapy, biomarkers that reveal key aspects of that biology have the potential to guide clinical decision making. The tumor genome is unique among all the possible sources of biomarkers. DNA structural and sequence aberrations provide a genomic fingerprint unique to each tumor recording the deviation of the tumor genome from its normal counterpart. These aberrations can reveal the key genes and pathways driving tumor growth. Pathways for bringing cancer genome analysis into the clinic will be discussed.Paul S. Meltzer, M.D., Ph.D., Head, Molecular Genetics Section and Branch Chief, National Cancer Institute

9:25 Unraveling the Genetic Basis of Cancer: Utility and Promise of Next Generation Sequencing in Target Discovery and Patient Stratification Human Cancer evolves through a series of genetic and epigenetic events that allow a normal cell to become transforming and spread to distant organs. The past few years have seen a dramatic change in our understanding of the genetic basis of human cancer, mostly driven by the advances made in next-generation sequencing technologies. Rapid and cost effective analysis of cancer genomes has started to not only bring new therapeutic targets to the surface, but also holds great promise in translating genetically targeted drugs and personalized medicines into the clinic. This presentation will give an overview of various NGS applications, ranging from discovery of synthetic lethal targets to its use in building hypotheses for patient selection.Markus Warmuth, M.D., Head of Oncology Drug Discovery, Cambridge, Novartis Institutes for BioMedical Research

10:00 Arch2POCM: A Drug Development Approach from Disease Targets to their Clinical Validation

Current siloed efforts in drug discovery can limit efforts placed on high-risk, high-opportunity targets being uncovered by genomic and network approaches. An alternative approach is being considered, where clinical target validation might occur within an open space where all could track and take advantage of the stream of information on a particular target. A linkage between public support, academia, regulators, and industry to maximize their intrinsic strengths and a redefined competitive/precompetitive space for drug discovery would be required.Stephen H. Friend, M.D., Ph.D., President, Co-Founder and Director, Sage Bionetworks



Wednesday, August 3, 2011 (continued)

3:30 New Frontiers in Cancer: Complete Sequencing of the Cancer GenomeComplete Genomics has sequenced the genomes of over 100 tumor-normal sample pairs from a variety of cancers using our unique high-throughput sequencing platform. By providing cancer researchers with sequencing results including small variations, structural variations, copy number variations and somatic mutation data, scientists can study the genetic basis of cancer without the cost and labor associated with building, operating, and maintaining large-scale sequencing and computing facilities. As the research community develops a deep understanding of the genetic causes of cancer, clinical-quality cancer genome sequencing offers dramatic new approaches to cancer detection and treatment.Rade Drmanac, Ph.D., Chief Scientific Officer, Complete Genomics, Inc.

4:00 Clinical High-Throughput Sequencing for Personalized Medicine: A Roadmap at MichiganWe envision integrating high throughput genomic and transcriptomic sequencing of cancer samples to match patients with the most appropriate therapies and clinical trials based on identification of actionable aberrations. Primary focus is on tumor specific gene fusions, mutations or outlier expression of genes involving known and investigational therapeutic targets. Additionally, the data will be used to address basic research questions of cancer heterogeneity, multiple driver aberrations/collaborating pathways and genetic basis of disease/responsiveness to therapy.Chandan Kumar-Sinha, Ph.D., Research Assistant Professor, Michigan Center for Translational Pathology, University of Michigan

4:30 Integrated Genomic Analysis of Cancer for Diagnosis, Prognosis, and PathogenesisVarious forms of genomic analysis are in common use to establish diagnosis, prognosis, or treatment, usually based on a single class of genomic features like gene expression. While useful, this limited approach likely underestimates the utility of a broader array of genomic features for these purposes. A comparative analysis of the use of a single class (mRNA expression) versus a suite of features, including coding and non-coding RNA, CNV, and LOH to establish diagnosis and prognosis in cancer is presented.Timothy J. Triche, M.D., Ph.D., Director, Center for Personalized Medicine, Children’s Hospital Los Angeles; Professor & Vice Chair, USC Keck School of Medicine

5:00 Close of Conference

Next-Generation Sequencing & Genomic Medicine

Present a Poster to Enhance Your Conference ExperienceSharing your research with your peers could lead to exciting opportunities for you to advance your career.. and it can help justify the time and cost of your attendance at the conference.

The deadline to submit an abstract & be included in the conference documentation is July 1, 2011 (full payment for conference and poster fee must be received by this date.) After that date posters are on a space available basis. New poster size: Maximum dimensions of 36” wide (3 feet) x 48” high 4 (feet) To submit your poster and for additional details on the poster sizes and regulations, please visit www.drugdisc.com

Academic Grant and Student Poster Award ProgramTo support the educational and professional development of academic researchers and students in this field, IBC Life Sciences will award 5 complimentary registrations and posterboard spaces for this year’s Drug Discovery & Diagnostic Development conference. The recipients will be selected by the conference advisory board, and each winner chosen will present their poster in the conference poster hall and receive a complimentary 3-Day Conference pass. Eligibility requirements and participation instructions are:

• Recipients must hold a full-time academic faculty/research position or be full-time graduate students at a university or academic research institute

• Winners must agree to present a poster. Poster abstracts and applications for this award program must be received no later than Friday, June 17, 2011 at: www.DrugDisc.com

* Poster viewing times will be scheduled during conference breaks and lunches in the poster/exhibit hall

• Winners will be notified by Friday, July 1, 2011 and those not awarded a complimentary registration will receive a discount to attend the conference at a substantially reduced academic/student rate

• Travel and lodging expenses are the responsibility of the recipient

Groups of 3 Save Up to 25% off Standard Registration Rate

Attendees can enjoy significant savings on standard registration rates when registering in groups. To save up to 25% off your group of three attendees from the same company, just select the “3 Person Group Rate” when registering. For groups of 4 or more, please contact 646-895-7445.


Venue & AccommodationsHyatt Regency San Francisco 5 Embarcadero Center, San Francisco, California, 94111 Tel: 415-788-1234 • Fax: 415-398-2567 Online Hotel Reservations Site: https://resweb.passkey.com/go/RSCH2011

Please call the hotel directly at 1-888-421-1442 before July 8, 2011 to be included in IBC’s dedicated room block for this conference. Please identify yourself as a participant in IBC’s conference on Drug Discovery to receive the reduced room rate. Be sure to make your reservation as soon as possible as rooms tend to fill up very quickly and all reservations are subject to availability.Hotel Reservation Policies: A first and last night non-refundable deposit is required at the time of reservation. Cancellations and changes to a reservation will be accepted without further financial responsibility up until 72 hours prior to your arrival date. Your credit card is subject to being charged for your full reservation if cancellation or changes to a reservation are received any less than 72 hours of your arrival date.

Additional Registration InformationConference Registration Substitutions/Cancellations: If you need to make any changes or have any questions, please feel free to contact us via email at [email protected]. Cancellations must be in writing and must be received by IBC prior to 10 business days before the start of the event. Upon receipt of a timely cancellation notice, IBC will issue a credit voucher for the full amount of your payment, which may be applied towards registration fees at any future IBC event held within 6 months after issuance (the “Expiration Date”). All credit vouchers shall automatically expire on the Expiration Date and shall thereupon become void. In lieu of issuance of a credit voucher, at your request, IBC will issue a refund less a $595 processing fee per registration. Registrants are advised that no credit vouchers or refunds will be issued for cancellations received 10 business days or less prior to start of the event, including cancellations due to weather or other causes beyond the Registrant’s control. IBC therefore recommends that registrants allow for unexpected delays in making travel plans. Substitutions are welcome at any time. If for any reason IBC decides to cancel this conference, IBC accepts no responsibility for covering airfare, hotel or other costs incurred by registrants, including delegates, sponsors, speakers and guests.

Additional Registration Information: Program content and speakers subject to change. Conference badges are non-transferable and lost badges will not be replaced without payment of the full conference registration fee. Please note that payment is required in advance of the conference. Please make check(s) (in U.S. funds drawn on a U.S. bank) payable to IBC Life Sciences and attach to the registration form.

SPECIAL NEEDS: If you have a disability or special dietary needs, please let us know in order that we may address your special needs for your attendance at this show. Please send your special needs via email to [email protected]

Standard Rate Industry Fees By May 20, 2011 By June 10, 2011 By July 15, 2011 After July 15, 2011

3-Day Conference (August 1-3) Best Value $1899 $1999 $2099 $2199

3 Person Group Rate $1649 each $1649 each $1759 each $1759 each (Valid for 3-day conference only)

2-Day Conference (August 1-2 or August 2-3) $1599 $1699 $1799 $1899

Standard Rate Academic/Govt. Fees* By May 20, 2011 By June 10, 2011 By July 15, 2011 After July 15, 2011

3-Day Conference (August 1-3) Best Value $749 $799 $849 $899

3 Person Group Rate $674 each $674 each $719 each $719 each (Valid for 3-day conference only)

2-Day Conference (August 1-2 or August 2-3) $649 $699 $749 $799* Academic rate is extended to full-time employees of government, universities & university-affiliated hospitals only.For on-site registrations, please add $100. See inside for policies regarding Substitutions, Cancellations and Special Needs.

To Reserve a Posterboard: Vendor/Supplier* $300 Pharma/Biotech $100 Academic/Government FREE*Vendor rate is for exhibiting/sponsoring companies and/or other posters that upon review are of commercial/product focus.

Explore New Technologies and Innovative Solutions in the Exhibit Hall

Bronze Sponsors

From sample preparation to data analysis, Agilent Technologies provides microarrays, reagents and a QPCR platform for multiple genomic applications,

along with the new SureSelect Target Enrichment Platform for next-gen sequencing. BGI (formerly Beijing Genomics Institute), founded in 1999, is now the largest genomic organization in the world. Our goal is to make leading-edge genomics highly accessible to the global research community by leveraging

industry’s best technology, economies of scale, and expert bioinformatics resources. This enables our customers and collaborators to quickly migrate from samples to discovery.

Technology Workshop Sponsors

Interactive Workshop Sponsor

Exhibit Hall Hours:August 2: 9:45 am – 4:15 pmAugust 3: 10:30 am - 3:30 pm

Exhibitors (as of March 10, 2011)

®

Why Exhibit or Sponsor at this Conference?• Reach Targeted Groups of Buyers Attending All Five Conferences

• Meet Senior Level Scientists and Executives from Pharma, Biotech and Academic Organizations all at one place, looking for new technologies and innovative solutions to accelerate their drug discovery and development efforts.

IBC will assist you in meeting all of your company objectives pre-event, onsite and post-event. Sponsorships currently available include: Technology Workshops , Receptions, Badge and Lanyards, Refreshment Breaks, Conference Sessions, Webinars, and more.

For more information download the exhibit/sponsor prospectus online at www.drugdisc.com or contact:

Sherry Johnson, Tel: 508-614-1451, E-mail: [email protected]

Your conference registration gives access to all content during the days you attend.

Registration Information


Industry Fees Standard Rate LRIG Member Rate

3-Day Conference (August 1-3) Best Value $2199 $1759

3 Person Group Rate (Valid for 3-day conference only) $1759 each NA

2-Day Conference (August 1-2 or August 2-3) $1899 $1519

Academic/Govt. Fees* Standard Rate LRIG Member Rate

3-Day Conference (August 1-3) Best Value $899 $719

3 Person Group Rate (Valid for 3-day conference only) $719 each NA

2-Day Conference (August 1-2 or August 2-3) $799 $639* Academic rate is extended to full-time employees of government, universities & university-affiliated hospitals only.For on-site registrations, please add $100. See inside for policies regarding Substitutions, Cancellations and Special Needs.

To Reserve a Posterboard: Vendor/Supplier* $300 Pharma/Biotech $100 Academic/Government FREE*Vendor rate is for exhibiting/sponsoring companies and/or other posters that upon review are of commercial/product focus.

Your conference registration gives access to all content during the days you attend.

Registration Information

LRIG Members Save 20% Off Standard RatesUse Priority Code D11203LRIG

How to Register: Online: www.drugdisc.com

Phone: (800) 390-4078 International Callers: US +1 941 554-3500

ibc’s 2nd annual next-generation sequencing & genomic ... · ibc’s 2nd annual...

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