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NGX Applying Next-Generation Sequencing

Cambridge Healthtech Institute’s

August 19-20

August 20-21

Sequencing Strategies for Success

Eighth Annual

Dynamics of the Microbiome on Health and Disease

Inaugural

Sequencing Data Analysis and Interpretation

Sixth Annual

Single-Cell SequencingInaugural

August 19-21, 2013 | Omni Providence Hotel | Providence, RIFinal Agenda

Corporate Sponsors: Corporate Support Sponsor: Healthtech.com/Sequencing

Conference-at-a-Glance

Short Courses/Plenary Keynote

Sponsor & Exhibit Opportunities




Single-Cell Sequencing

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Conference-at-a-GlanceMonday, August 19 morning Pre-Conference Short Courses*

Monday, August 19 afternoon Sequencing Strategies for Success Dynamics of the Microbiome on Health and Disease

Monday, August 19 evening Evening Networking Reception

Tuesday, August 20 morning Sequencing Strategies for Success Dynamics of the Microbiome on Health and Disease

Tuesday, August 20 afternoon Plenary Keynote Session

Tuesday, August 20 evening Dinner Short Courses*

Wednesday, August 21 morning Single-Cell Sequencing Sequencing Data Analysis and Interpretation

Wednesday, August 21 afternoon Single-Cell Sequencing Sequencing Data Analysis and Interpretation

*Separate Registration Required

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MoNDAy, AuguST 19, 9:00 AM-12:00 PM

SC1: Mapping genomes in 3DGenomes are organized into 3-dimensional (3D) conformation in vivo through interactions with protein factors. In addition, DNA elements separated by long genomic distances are known to functionally interact. However, the details of these 3D structures and their role in gene transcription are largely unknown. This course is designed to provide an overview of sequencing strategies and analysis for probing the 3D structure of genomes.Jennifer E. Phillips-Cremins, Ph.D., Research Scientist, Job Dekker Laboratory, Program in Systems Biology, University of Massachusetts Medical SchoolYijun Ruan, Ph.D., Professor and Director for Genome Sciences, Jackson Laboratory for Genomic Medicine, The Jackson LaboratoryChia-Lin Wei, Ph.D., Group Lead, Sequencing Technologies, DOE Joint Genome Institute

SC2: Sample PrepThe emergence of next-generation sequencing technologies has revolutionized genomic research. This dramatic advancement, however, still involves complicated and labor-intensive workflows for upstream sample preparation, library construction, and template amplification. Instructors share their solutions to prepare for sequencing runs (including the specific requirements of sequencing platforms) by addressing customizability, compatibility, and cost effectiveness.Stacey Broomall, Biologist, R&T, U.S. Army, Edgewood Chemical Biological Center

John-David Herlihy, Ph.D., Product Manager, Covaris, Inc.Alexander Seitz, M.D., CEO, LexogenMichael Vishnevetsky, Ph.D., Vice President, WaferGen Biosystems, Inc.

TuESDAy, AuguST 20, 6:00-9:00 PM

SC3: Assembly and AlignmentThe most important first step in understanding next-generation sequencing data is the initial alignment or assembly. This course is designed to provide an overview of alignment and assembly algorithms, and comparisons for various applications.Gabe Rudy, Vice President, Product Development, Golden Helix and Author, “A Hitchhiker’s Guide to Next Generation Sequencing”

*Separate Registration Required

Short Courses*

Jeffery A. Schloss, Ph.D., Director, Division of genome Sciences, National Human genome Research Institute, National Institutes of Health

Dr. Schloss, in addition to his role at NIH, manages a grants program to develop technologies with which to sequence human genomes for $1,000 and coordinates the Centers of Excellence in Genomic Science program. He helped formulate and then led or served on interdisciplinary initiatives, including the NIH Bioengineering Consortium (BECON), the Trans-NIH Nano Task Force and the U.S. interagency National Nanotechnology Initiative.

David galas, Ph.D., Principal Scientist, Pacific Northwest Diabetes Research InstituteBefore joining Pacific Northwest

Diabetes Research Institute, Dr. Galas was Professor and Senior Vice President at the Institute for Systems Biology, Chancellor and Norris Professor of Applied Life Science at the Keck Graduate Institute and Professor and Chairman of Molecular Biology at the University of Southern California. Involved in translating science into diagnostics and therapeutics in several biotechnology companies, he researches human genetics of complex diseases and the development and application of new technologies and computational methods. He has served on the NRC Board on Life Science, among other groups, and is a lifetime Associate of the National Academy of Sciences.

Sherman Weissman, Ph.D., Sterling Professor of genetics and Medicine, yale university School of MedicineDr. Weissman has long

contributed to studies of the molecular biology of higher cells, focusing on the globin and MHC loci. Early accomplishments include identification of sequences for transcription termination and initiation for E. coli RNA polymerase and the sequencing of the SV40 virus. His lab has worked extensively on cDNA technology and has been developing methods for genome-scale analysis of individual and small numbers of cells. Widely experienced in genomic technology, Dr. Weissman has co-directed the Yale Center for Genomics and Proteomics, worked to develop technical approaches that can be applied to large-scale analysis, and participated in the NIHGR ENCODE project since its inception.

yaniv Erlich, Ph.D., Principal Investigator, Whitehead Fellow, Whitehead Institute for Biomedical ResearchDr. Erlich earned his Ph.D.

from the Watson School of Biological Sciences at Cold Spring Harbor Laboratory in 2010 and has received the Harold M. Weintraub Award, the IEEE/ACM-CS HPC Award, Goldberg-Lindsay Fellowship and Wolf Foundation Scholarship for Excellence in Exact Sciences. His research interests lie in computational human genetics and he was selected to be part of the 2010 Tomorrow’s PIs team by Genome Technology.

Plenary Keynote Session

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NGX Sequencing Strategies for Success Delivering Genomes at Exponential Rates

August 19-20, 2013Eighth Annual

As prices continue to drop and technology continues to improve, the purchase of a next-generation sequencing (NGS) platform is now a reality for most research laboratories. Once you have purchased a platform, however, how do you maximize the greatest potential for your investment? Realizing this potential requires efficient workflow strategies, careful experimental design, comprehensive targeted enrichment technologies, data analysis, management, and integration, in addition to maintaining your platform and people management all at maximum production. The central theme at CHI’s Sequencing Strategies for Success conference is efficient utilization of your NGS platform. Sessions will focus on common bottlenecks, case studies, real-world experiences and solutions from experienced NGS users.

MoNDAy, AuguST 19

8:30 am Short Course Registration and Morning Coffee

9:00-12:00 pm Short Courses* (see page 3 for details)SC1: Mapping Genomes in 3DSC2: Sample Prep

1:00 Main Conference Registration

Sequencing Centers

2:00 Chairperson’s opening RemarksLisa D. White, Ph.D., Associate Professor, Molecular and Human Genetics, Baylor College of Medicine

2:10 Sequencing: Wonderful Adventure or Terrible Tragedy?Lisa D. White, Ph.D., Associate Professor, Molecular and Human Genetics, Baylor College of MedicineApplying next-generation sequencing (NGS) to clinical diagnostics promises to increase the rate of diagnoses, and as more correlations with phenotype are drawn, there is the promise of biomarker detection for prognosis and therapeutics. Taking NGS to the next step from a basic research procedure in a non-certified molecular lab to providing clinical sequencing requires a host of different procedures and a different laboratory culture than that found in basic research. The experience of launching NGS in a laboratory can run the gamut of wonderful adventure to terrible tragedy depending on preparedness, resources and support. This talk will cover some of the issues required to make the transition into an NGS CLIA-/CAP-certified laboratory.

2:40 Translational Science: From Basic Research to genomic Medicine in an Academic Core Laboratory – Lessons LearnedNicholas P. Ambulos, Jr., Ph.D., Associate Professor, Microbiology and Immunology; Executive Director, School of Medicine Core Facilities; Director, Genomics Core Facility, University of Maryland School of MedicineNext-generation sequencing technology continues to improve and become more cost-effective. Academic core laboratories have played a significant role in making this technology readily available to basic research laboratories. As a result, this technology is rapidly becoming the diagnostic tool of choice for many clinicians. The challenge we now face is how these academic core laboratories can provide comprehensive support to basic research, translational studies and clinical diagnostics and play a role in educating healthcare professionals.

3:10 An overview of the New york genome CenterKevin V. Shianna, Ph.D., Senior Vice President, Sequencing Operations, New York Genome CenterThe NYGC initiated its sequencing operations in early 2012 and is building out to be one of the largest genome centers in North America. An overview of our experience to date will be presented along with future goals and challenges.

3:40 Refreshment Break

4:00 Combining Forces: using All NgS Platforms to Advance Cancer Research at CgRJoseph Boland, Director, Research and Development, Cancer Genomics Research Laboratory,

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Frederick National Laboratory for Cancer Research, National Institutes of HealthWith the continual reduction in instrument costs and comparable quality metrics, the Cancer Genomics Research Laboratory (CGR) has put in place a combined approach to cancer research utilizing our Ion Proton/PGMs in conjunction with our Illumina HiSeqs/Miseqs. Our presentation will highlight comparative experiments between Illumina and Life instruments, the current wet-lab processes using this combined approach—such as our combined exome, exome follow-up and transcriptome pipelines—and how we see this impacting our future research.

4:30 From genome Technology to genome BiologyYijun Ruan, Ph.D., Professor and Director for Genome Sciences, Jackson Laboratory for Genomic Medicine, The Jackson LaboratoryAt the Jackson Laboratory, we have developed a dynamic genomics program with a focus on genomic technologies based on paired-end-tag (PET) sequencing, which has broad applications in various genome biology questions including RNA-PET for transcriptome, DNA-PET for genome structural variation and de novo genome sequence assembling, and ChIP-PET and ChIA-PET for genome regulation. We are applying the PET sequencing approaches for studies of transcription regulatory mechanisms in human and mouse genomes, identification of genetic variations and fusion genes in patient-specific cancer genomes and characterization of new genomes from a wide range of organisms including bacteria, animals and plants. Our recent studies of identifying patient-specific genomic variations, 3D mapping of the promoter interactions in human genomes and de novo assembling of plant genomes will be highlighted.

5:00 Panel Discussion with Afternoon SpeakersModerator: Lisa D. White, Ph.D., Associate Professor, Molecular and Human Genetics, Baylor College of MedicinePanelists:Nicholas P. Ambulos, Jr., Ph.D., Associate Professor, Microbiology and Immunology; Executive Director, School of Medicine Core Facilities; Director, Genomics Core Facility, University of Maryland School of MedicineKevin V. Shianna, Ph.D., Senior Vice President, Sequencing Operations, New York Genome CenterJoseph Boland, Director, Research and Development, Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, National Institutes of HealthYijun Ruan, Ph.D., Professor and Director for Genome Sciences, Jackson Laboratory for Genomic Medicine, The Jackson Laboratory

5:45 Welcome Reception in the Exhibit Hall

6:45 Close of Day

TuESDAy, AuguST 20

7:30 am Breakfast Technology Workshop (Sponsorship Opportunity Available)

Tools, Tips ‘n Tricks

8:15 Chairperson’s RemarksMats Ljungman, Ph.D., Associate Professor, Radiation Oncology, University of Michigan

8:20 Functional Analysis of the Nascent Transcriptome using “Run-on” Sequencing Methods: Looking Beyond the Pipeline

Hojoong Kwak, M.D., Research Scientist, Molecular Biology and Genetics, John Lis Laboratory, Cornell UniversityWe have recently developed a series of nascent RNA sequencing that identifies the active RNA polymerase with extreme sensitivity and up to base pair resolutions named GRO-seq and PRO-seq. First-pass processing of the “run-on” sequencing data uses the common “pipelines” established for RNA-seq or ChIP-seq. We present a few of our next-level analyses of various functional aspects of RNA polymerase machinery, such as the high-resolution pausing patterns and elongation rates.

8:50 RNA-Seq for Enrichment and Analysis of IRF5 Transcript Expression in SLEBetsy J. Barnes, Ph.D., Associate Professor, Biochemistry and Molecular Biology, New Jersey Medical School University Hospital Cancer Center, University of Medicine and Dentistry New JerseyThis presentation will discuss enriched RNA-seq for the rapid identification and quantification of differentially spliced transcript variants in primary immune cells from genotyped healthy donors and patients with systemic lupus erythematosus (SLE). This technique enabled the identification of an IRF5 transcript signature that associates with patients carrying the IRF5-SLE risk haplotype.

9:20 Bru-Seq and BruChase-SeqMats Ljungman, Ph.D., Associate Professor, Radiation Oncology, University of MichiganBru-Seq and BruChase-Seq are based on the metabolic pulse-chase labeling of nascent RNA with bromouridine followed by isolation of Bru-labeled RNA and deep sequencing. While Bru-Seq informs us on the relative rates of RNA synthesis genome-wide, BruChase-Seq assesses the kinetics of splicing and the relative stability of all transcripts. These techniques have revealed an astonishing wealth of information about the complexities of expression of coding and non-coding RNA in human cells as well as splicing kinetics, elongation rates, transcription start sites and transcription from enhancer elements.

9:50 Selected oral Poster Presentation: Cross-Contamination Monitoring using a unique Sequence Spike-In ControlRichard A. Moore, Ph.D., Sequencing Group Leader, Genome Sciences Centre, British Columbia Cancer AgencyAs sample numbers have increased, and clinical re-sequencing has developed, it has become essential to include quality control measures to exclude compromised samples. This requires accurate identification of cross-contamination and sample swaps throughout the pipeline, as well as close monitoring of sample identity. We have developed a panel of unique DNA sequences cloned into a common vector (>1000 verified). These are added to the sample when it is first received and can be detected with a simple PCR and sequencing from any stage of the process. Sequence reads derived from this spike-in are generated along with the standard sequencing run and are used to confirm sample identity and determine cross-contamination levels. Successful spiking directly into blood and tissue samples prior to DNA extraction has been demonstrated. This methodology has been implemented in our targeted clinical diagnostic pipeline and has also been successfully validated for whole-genome sequencing. It is a very inexpensive, flexible and platform-agnostic solution to a pressing need.

10:05 Coffee Break in the Exhibit Hall with Poster Viewing

11:00 using Multiplex ChIP-Seq to Explore Centromere Evolution in Budding yeastPhilippe Lefrancois, Ph.D., Faculty of Medicine, University of Montreal

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We applied multiplex ChIP-Seq to characterize Saccharomyces cerevisiae kinetochore proteins directly and indirectly binding to chromatin, in multiple genotypes. In this organism carrying 126-bp, point centromeres, we discovered regions with centromeric activity elsewhere in the genome when the levels of a centromeric histone are elevated. These novel regions, sharing characteristics of both point and larger regional centromeres, have important implications for the evolution of centromeres.

11:30 Design and Analysis of CLIP-Seq Experiments for Identifying Targets and Functions of RNA-Binding ProteinsAnastasios Vourekas, Ph.D., Research Scientist, Pathology and Laboratory Medicine, Perelman School of Medicine, University of PennsylvaniaIn vivo crosslinking of RNA-protein complexes and high-throughput sequencing of fragments of these RNAs is revolutionizing the way RNA-binding proteins are studied. This method provides transcriptome-wide landscapes of RNA targets bound in vivo with nucleotide-level resolution. I will present guidelines and examples for the design and data analysis of CLIP-seq experiments and how these can lead to a comprehensive understanding of the functions of diverse RNA-binding proteins.

12:00 pm Rapid Assembly and Analysis of Clinical Sponsored by Sequence Data: using DNASTAR Software to Identify Disease-Causing MutationsMatthew Keyser, Next-Gen Applications Scientist, DNASTAR, Inc.DNASTAR offers an integrated suite of software for assembling and analyzing clinical sequencing data on a desktop computer. In this example, we align exome data from a disease and control group to the human genome using DNASTAR software. After alignment, the same software package is used to view the results and identify SNPs and genes of interest.

12:30 Close of Session

12:30 From Reads to Variants: Ten-Fold Reduction in Time Sponsored by and Cost with Improved AccuracyRupert Yip, Ph.D., Director, Product Marketing, Bina TechnologiesAlignment and variant calling of raw NGS reads has been plagued by expensive HPC hardware and the bioinformatics personnel to support and maintain home-grown, open-source secondary analysis solutions. Such solutions can take up to weeks and $1000s per analysis. We present a genomic analysis platform that reduces, by ten-fold, the time and cost for secondary analysis while improving accuracy compared to standard pipelines. Our innovative model reduces costs by ten-fold while preventing hardware obsolescence.

PLENARy KEyNoTE SESSIoN

2:00 Chairperson’s opening RemarksToby Bloom, Ph.D., Deputy Scientific Director, Informatics, New York Genome Center

2:10 A Revolution in DNA Sequencing Technologies: Challenges and opportunitiesJeffery A. Schloss, Ph.D., Director, Division of Genome Sciences, National Human Genome Research Institute, National Institutes of HealthThe initial sequencing of the human genome spurred an appetite for much more human sequence information to better understand the contributions of human sequence variation to health and disease. However, despite dramatic reductions during the Human Genome Project, the cost of sequencing was clearly too high to collect the very large numbers of human and numerous other

organism genome sequences needed to achieve that understanding. In 2004, NHGRI launched parallel programs to reduce the cost of sequencing a mammalian genome initially by two (in five years), and eventually by four orders of magnitude (in ten years). This presentation will summarize the technologies that are in high-throughput use to produce stunning amounts of sequence and related data and novel biological insights, and will emphasize technologies currently emerging and on the horizon that may provide human genome sequence data with the nature, quality, cost and turnaround time needed for applications in research and medicine.

2:50 RNA is Everywhere: Characterizing the Spectra and Flux of RNA in Mammalian CirculationDavid Galas, Ph.D., Principal Scientist, Pacific Northwest Diabetes Research InstituteThe discovery of foreign RNA in blood and tissues of humans and mice raises many questions, including its origins, the mechanisms of its transport and stability and what, if any, functions it has. I will discuss what we know about circulating exRNA in human plasma and the use of NGS in the exploration of this new area of investigation in biology and medicine.

3:30 Refreshment Break in the Exhibit Hall with Poster Viewing

4:15 genomics and the Single CellSherman Weissman, Ph.D., Sterling Professor of Genetics and Medicine, Yale University School of MedicineStudies of single cells are being approached by widely different methods, principally either florescence microscopy including super-high resolution methods, cloning and expansion of single cells or most generally applicable, genomic-scale nucleic acid analyses. The last includes single-cell DNA sequence analysis, gene expression analysis and most recently analyses of telomere length, DNA methylation and potentially closed regions of chromatin. Also, in the near future, it may be possible to combine several analyses of a single cell, including mRNA expression, genomic DNA methylation and protein secretion. These approaches will have major value for diverse fields, including molecular analysis of the early stages of development, the nature and heterogeneity of stem cells and transient repopulating cells in various systems including the hematopoietic system, the nature and extent of heterogeneity of neurons, heterogeneity in neoplasia and in functional subsets of cells of the immune system. A substantial experimental challenge is to distinguish technical variation from stochastic and deterministic events in single cells. Another, broader challenge is to correlate the results of genomic properties that necessarily involve destruction of the cell with the functional properties and potential of the individual cell being analyzed. These issues will be discussed briefly in the presentation.

4:55 genome HackingYaniv Erlich, Ph.D., Principal Investigator, Whitehead Fellow, Whitehead Institute for Biomedical ResearchSharing sequencing datasets without identifiers has become a common practice in genomics. We developed a technique that uses entirely free, publicly accessible Internet resources to fully identify individuals in these studies. I will present quantitative analysis about the probability of identifying U.S. individuals by this technique. In addition, I will demonstrate the power of our approach by tracing back the identities of multiple whole-genome datasets in public sequencing repositories.

5:35 Close of Sequencing Strategies for Success Conference / Short Course Registration open

6:00-9:00 Dinner Short Course* (see page 3 for details)SC3: Assembly and Alignment

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NGX Dynamics of the Microbiome on Health and DiseaseCommunities, Composition, and Computation

August 19-20, 2013Inaugural

Advances in next-generation sequencing and computation have elucidated the impact of human genomic variation; however, the impact of this variation is largely unexplored in the human microbiome. Now clinical and environmental researchers have the high-resolution tools to explore the emergent science of microbial communities and the ecosystems they inhabit. CHI’s Dynamics of the Microbiome on Health and Disease conference focuses on understanding the role of the microbiome to offer new insights into disease processes and discovery of new therapeutic strategies.

MoNDAy, AuguST 19

8:30 am Short Course Registration and Morning Coffee

9:00-12:00 pm Short Courses* (see page 3 for details)SC1: Mapping Genomes in 3DSC2: Sample Prep

1:00 Main Conference Registration

Communities and Composition

2:00 Chairperson’s opening RemarksEmma Allen-Vercoe, Ph.D., Assistant Professor, Molecular and Cellular Biology, University of Guelph

» FEATuRED PRESENTATIoN

2:10 Metagenomic Platforms for Diagnostic, Microbial Composition and Etiologic Agent Discovery ApplicationsJoseph Petrosino, Ph.D., Assistant Professor, Molecular Virology and Microbiology; Director, Alkek Center for Metagenomics and Microbiome Research, Baylor College of MedicineMetagenomics strategies for etiologic agent discovery and diagnostic detection have multiple advantages over past methods: they are highly sensitive; they are able to detect sub-PFU levels of viruses in clinical samples; there is no requirement for propagation of the suspected agent in the laboratory; and there is no need for prior knowledge of the agent to be detected. For suspected bacterial agents we are using 16S rRNA gene and whole-genome shotgun surveys of diverse human samples to identify potential agents and antibiotic resistance profiles. For suspected viral agents we are sequencing randomly primed cDNA libraries and querying these data against a custom viral

database. Our results show several new potential bacterial agents that may be associated with different diseases with unknown etiologies. We are currently in the process of translating these methods to the clinic where these approaches can immediately impact human health.

2:40 Archaea and Fungi of the Human gut MicrobiomeChristian Hoffmann, Research Scientist, Frederic D. Bushman Laboratory, Microbiology, Perelman School of Medicine, University of PennsylvaniaWe investigate associations of diet with fungal and archaeal populations in the gut microbiome, as well as interdomain relationships between bacteria, archaea and fungi in a cohort of 96 individuals. Diet relationships with microbial taxa were investigated regarding usual and recent dietary intake.

3:10 Microbial Ecosystems Therapeutics: A New Paradigm in Medicine?Emma Allen-Vercoe, Ph.D., Assistant Professor, Molecular and Cellular Biology, University of GuelphIt is now clearly recognized that the human gut microbial ecosystem is a critical factor in the maintenance of host health, and that disturbances in this ecosystem, leading to enduring imbalance (dysbiosis) are associated with an ever increasing number of disorders (for example, IBD, IBS, diabetes, asthma, autism). With this in mind, is it possible to harness the microbial

Alumni Discount SAVE 20%Cambridge Healthtech Institute (CHI) appreciates your past participation at our events. Through loyalty like yours, CHI has been able to build this event into a must-attend for senior-level decision makers. As a result of the great loyalty you have shown us, we are pleased to extend to you the exclusive opportunity to save an additional 20% off the registration rate. Just check off the box marked Alumni Discount on the registration form to receive the discount!

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ecosystems of supremely healthy individuals to correct gut dysbiosis in diseased individuals? I will present the “brave new future” of microbial ecosystem therapeutics and outline the questions that need to be considered before the practice can be put into mainstream use.

3:40 Refreshment Break

4:00 Studying the Human Microbiome with Citizen ScienceGabriel Foster, Vice President, Lab Operations, uBiomeuBiome is a citizen science startup that uses next-generation sequencing to examine the microbial ecology in humans. We crowdfunded our startup and will involve the public in asking and answering questions about the human microbiome.

4:30 An Active Subset of the Human gut Microbiota Responsive to XenobioticsCorinne Maurice, Ph.D., Research Scientist, Peter J. Turnbaugh Laboratory, FAS Center for Systems Biology, Harvard UniversityThe human gut contains trillions of microbes that can influence the efficacy and toxicity of therapeutic drugs, including antibiotics. However, the identity of the metabolically active cells and their responsiveness to drug exposure remains unclear. Here, we identify the Firmicutes as the active cells of the gut microbiota, rapidly affected by host-targeted drugs and antibiotics. Xenobiotics exposure increased cell damage and induced the expression antibiotic resistance, drug metabolism and stress response genes. This study highlights the many unintended consequences of therapeutics on the activity of our resident gut microbes.

5:00 Panel Discussion with Afternoon SpeakersModerator: Emma Allen-Vercoe, Ph.D., Assistant Professor, Molecular and Cellular Biology, University of Guelph Panelists:Joseph Petrosino, Ph.D., Assistant Professor, Molecular Virology and Microbiology; Director, Alkek Center for Metagenomics and Microbiome Research, Baylor College of MedicineChristian Hoffmann, Research Scientist, Frederic D. Bushman Laboratory, Microbiology, Perelman School of Medicine, University of PennsylvaniaGabriel Foster, Vice President, Lab Operations, uBiomeCorinne Maurice, Ph.D., Research Scientist, Peter J. Turnbaugh Laboratory, FAS Center for Systems Biology, Harvard University

5:45 Welcome Reception in the Exhibit Hall

6:45 Close of Day

TuESDAy, AuguST 20


Computation

8:15 Chairperson’s RemarksAleksandar Milosavljevic, Ph.D., Professor, Molecular and Human Genetics, Baylor College of Medicine


8:20 Principled Probabilistic Machine Learning Models for Analyzing Microbiome Time-Series Data

Georg K. Gerber, M.D., Ph.D., MPH, Instructor in Pathology, Harvard Medical School; Co-Director, Center for Clinical and Translational Metagenomics, Director, Computational Unit, Associate Pathologist, Center for Advanced Molecular Diagnostics, Pathology, Brigham and Women’s HospitalAlthough longitudinal microbiome data have the potential to yield new insights into the mechanisms by which the microbiota interact over time with immunologic and other dynamically varying host responses, methods for analyzing these data remain underdeveloped. To address this challenge, we present a machine learning framework that uses continuous-time dynamical models coupled with Bayesian dimensionality adaptation methods to simultaneously infer time-dependent signatures for individual taxa and assignments of taxa to functional groups. This framework enables several new types of analyses, including quantitation of the diversity of time-dependent microbial responses to perturbations, estimation of times required for members of host ecosystems to equilibrate after a perturbation event and automatic identification of sub-communities of microbes within the larger ecosystem that exhibit coordinated responses to perturbations. We demonstrate the application of our tools to two studies measuring changes over time in human or mouse gut flora in response to antibiotic pulses or challenge with an enteric pathogen, and additionally present extensions to our framework, including methods for automated experimental design that leverage data from pilot studies to develop optimized designs for larger studies, and for inference of latent continuous-time processes for correlation with time-dependent host physiologic or immunologic responses.

8:50 genboree Workbench and Network for Integrative Microbiome AnalysisAleksandar Milosavljevic, Ph.D., Professor, Molecular and Human Genetics, Baylor College of MedicineNext-generation sequencing is providing access to multiple layers of “omic” information, including genomic, epigenomic, transcriptomic and metagenomic layers. We present tools for microbiome analysis (16S and metagenome sequencing) deployed through the Genboree Workbench along with the toolsets for other “omic” assays. We also review the need for virtual integration of physically distributed data, tools and computing resources and the solution offered by the Genboree Network.

9:20 An EM Algorithm for Maximum Likelihood Estimation of Community Composition from Short-Read Sequencing DataJohn Novembre, Ph.D., Associate Professor, Human Genetics, University of ChicagoEstimation of the relative abundance of strains is a central challenge in microbiome studies. Using an EM-based algorithm that explicitly models sequencing error and multinomial sampling of reads and that in effect uses “soft” assignments of reads to strains, we are able to estimate reads with higher accuracy than methods that use “hard” assignments. We demonstrate the method’s performance in various scenarios using simulation and real data.

9:50 Selected oral Poster Presentation: A Novel Approach to unknown Pathogen Detection in Clinical SamplesSadie La Bauve, Ph.D., Bioenergy and Defense Technologies, Sandia National Laboratories


11:00 SPA: A Short Peptide Assembler for Metagenomic DataShibu Yooseph, Ph.D., Associate Professor, Informatics, J. Craig Venter InstituteThe availability of full-length protein sequences is extremely beneficial to any metagenomic data analysis as this allows for an accurate reconstruction of the functional and metabolic potential of the microbial community being studied. However, inference of long protein

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sequences from contigs obtained via a de novo assembly of nucleotide reads is hampered by the observation that metagenomic assemblies are often very fragmented. We describe a new method for reconstructing complete protein sequences directly from metagenomic data generated using Next Generation Sequencing technologies. Our framework is based on a novel Short Peptide Assembler (SPA) that uses a de Bruijn graph formulation to assemble protein sequences from their constituent peptide fragments identified on short reads. Using large simulated and real metagenomic datasets, we show that our method outperforms the alternate approach of identifying genes on nucleotide sequence assemblies, and generates longer protein sequences that can be more effectively analyzed.

11:30 observing Both the Forest and the Trees: Building Metagenomic Analysis Workflows with MetAMoSTodd Treangen, Ph.D., Senior Bioinformatics Scientist, National Biodefense Analysis and Countermeasures Center, Center for Bioinformatics and Computational Biology, University of MarylandI will present MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, allowing the user to simultaneously observe the forest (relative abundance estimation, functional landscape) and the trees (genome assemblies, annotated genes, variant motifs). Additionally, MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost.

12:00 pm Technology Spotlight (Sponsorship Opportunity Available)

12:15 Close of Session


»PLENARy KEyNoTE SESSIoN


2:10 A Revolution in DNA Sequencing Technologies: Challenges and opportunitiesJeffery A. Schloss, Ph.D., Director, Division of Genome Sciences, National Human Genome Research Institute, National Institutes of HealthThe initial sequencing of the human genome spurred an appetite for much more human sequence information to better understand the contributions of human sequence variation to health and disease. However, despite dramatic reductions during the Human Genome Project, the cost of sequencing was clearly too high to collect the very large numbers of human and numerous other organism genome sequences needed to achieve that understanding. In 2004, NHGRI launched parallel programs to reduce the cost of sequencing a mammalian genome initially by two (in five years), and eventually by four orders of magnitude (in ten years). This presentation will summarize

the technologies that are in high-throughput use to produce stunning amounts of sequence and related data and novel biological insights, and will emphasize technologies currently emerging and on the horizon that may provide human genome sequence data with the nature, quality, cost and turnaround time needed for applications in research and medicine.





5:35 Close of Dynamics of the Microbiome on Health and Disease Conference / Short Course Registration open


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NGX Single-Cell SequencingMeeting the Challenge One Cell at a Time

August 20-21, 2013Inaugural

Over the past decade, NGS technologies have moved at a rapid pace, dramatically reducing costs, and making genome sequencing more routine. What was once unthinkable is now possible. However, most genomes are still sequenced from DNA extracted from multiple cells, which misses differences between cells that could be crucial in controlling gene expression, cell behavior, and drug response. Still, challenges for single-cell sequencing remain, including cell isolation, DNA amplification, and bioinformatics. As the techniques are being refined, subtle differences between cells, such as the tiny genomic rearrangements, will emerge. CHI’s Single-Cell Sequencing conference focuses on the links between cell variation in tissues and organ function and further elucidates the origins of diseases.

TuESDAy, AuguST 20

12:00 pm Main Conference Registration


TuESDAy, AuguST 20



2:10 A Revolution in DNA Sequencing Technologies: Challenges and opportunitiesJeffery A. Schloss, Ph.D., Director, Division of Genome Sciences, National Human Genome Research Institute, National Institutes of HealthThe initial sequencing of the human genome spurred an appetite for much more human

sequence information to better understand the contributions of human sequence variation to health and disease. However, despite dramatic reductions during the Human Genome Project, the cost of sequencing was clearly too high to collect the very large numbers of human and numerous other organism genome sequences needed to achieve that understanding. In 2004, NHGRI launched parallel programs to reduce the cost of sequencing a mammalian genome initially by two (in five years), and eventually by four orders of magnitude (in ten years). This presentation will summarize the technologies that are in high-throughput use to produce stunning amounts of sequence and related data and novel biological insights, and will emphasize technologies currently emerging and on the horizon that may provide human genome sequence data with the nature, quality, cost and turnaround time needed for applications in research and medicine.



4:15 genomics and the Single CellSherman Weissman, Ph.D., Sterling Professor of Genetics and Medicine, Yale University School of MedicineStudies of single cells are being approached by widely different methods, principally either florescence microscopy including super-high resolution methods, cloning and expansion

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of single cells or most generally applicable, genomic-scale nucleic acid analyses. The last includes single-cell DNA sequence analysis, gene expression analysis and most recently analyses of telomere length, DNA methylation and potentially closed regions of chromatin. Also, in the near future, it may be possible to combine several analyses of a single cell, including mRNA expression, genomic DNA methylation and protein secretion. These approaches will have major value for diverse fields, including molecular analysis of the early stages of development, the nature and heterogeneity of stem cells and transient repopulating cells in various systems including the hematopoietic system, the nature and extent of heterogeneity of neurons, heterogeneity in neoplasia and in functional subsets of cells of the immune system. A substantial experimental challenge is to distinguish technical variation from stochastic and deterministic events in single cells. Another, broader challenge is to correlate the results of genomic properties that necessarily involve destruction of the cell with the functional properties and potential of the individual cell being analyzed. These issues will be discussed briefly in the presentation.


5:35 Short Course Registration


WEDNESDAy, AuguST 21


Technology Aids Single-Cell Investigation

8:15 Chairperson’s RemarksXinghua Pan, Ph.D., M.D., Associate Research Scientist and Group Head, Genetics, Yale University School of Medicine


8:20 Technology Progress and Prospect on Single-Cell genomicsXinghua Pan, Ph.D., M.D., Associate Research Scientist and Group Head, Genetics, Yale University School of MedicineHigh-throughput sequencing of the genomes and functional genomics elements for single cells is a new dimension for biological analysis. For these analyses, sensitive and faithful amplification technology is essential and difficult. We have developed a series of novel methods to generate sufficient materials for sequencing analysis, representing a full-length mRNA transcriptome, whole CpG methylome, whole genome and open chromatins. We have

also established a robust measurement of telomere length for single cells and a proof-of-concept process for analysis of DNA and RNA from the same single cell. The current progresses, applications and prospects will be addressed.

8:50 Strand-Seq: Template Strand Sequencing for High-Resolution Mapping of DNA Rearrangements in Single CellsEster Falconer, Ph.D., Research Fellow, Terry Fox Laboratory, BC Cancer Research CentreCurrent single-cell sequencing techniques can mask certain genomic features such as sister chromatid exchanges (SCE) and translocations, both of which signify genomic instability, a potent driver of malignancies. We show that sequencing only the original parental template strands (Strand-Seq) in single murine and human cells can map such events with much greater resolution than traditional cytogenetic techniques, with the exchange region mapped as close as 22 bp. Importantly, Strand-Seq libraries show that the current assemblies of the mouse and human reference genomes contain multiple incorrectly oriented contigs, which in the case of the mouse genome assembly, totals nearly 1% of the genome. I will discuss how Strand-Seq can dramatically expand the range of biological questions that can be addressed in single cells.

9:20 RNA-Seq and Find: Entering the RNA Deep FieldLior Pachter, Ph.D., Professor, Mathematics, Molecular & Cell Biology, and Electrical Engineering & Computer Science, University of California, Berkeley

9:50 Selected oral Poster Presentation: genome Assembly using Single-Cell DNA Template Strand DataMark Hills, Ph.D., Research Scientist, Terry Fox Laboratory, BC Cancer Research CentreStandard genome-building approaches create ever-increasing scaffolds that are built into new reference genomes. However, the return of these endeavors diminishes as the proportion of unsequenced regions decreases. Using Strand-seq, a method to sequence template strands in single cells, we show we can stratify and orient contigs from early- and late-assembly genomes. The direction of these template strands provides a unique chromosomal signature, such that contigs originating from the same chromosomes share the same template strand directionality. Using this approach we have fine-tuned the assembly of “completed” reference genomes of mouse and man, and demonstrate the ability to correctly rebuild chromosomes from contigs based solely on their template strands in an early mouse build (mm1). We can further stratify these contigs into relative orders using sister chromatid exchanges to infer genetic distances, and suggest that this strategy will find broad application in constructing genome assemblies in the future.


11:00 Diagnostic uses of Single-Cell genomicsAllison Welsh, Ph.D., Research Scientist, Genitourinary Oncology, Memorial Sloan-Kettering Cancer Center and Cold Spring Harbor LaboratoryThe ability to perform genomic assays on single cells provides a means to detect cancer initiation at its earliest stages and to follow response therapy using minimally invasive techniques. We will describe results from whole genome assays on blood (circulating tumor cells), urine and fine needle aspirates using NextGen sequencing to assess copy number variation (CNV) as well as specific point mutations in multiple cancer types.

11:30 Single-Cell Sequencing of Circulating Tumor Cells from Lung Adenocarcinoma Patients

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Fan Bai, Ph.D., Assistant Professor, Biodynamic Optimal Imaging Center, Peking UniversityWe performed single-cell sequencing of circulating tumor cells from patients with lung adenocarcinoma. The genetic profiles of CTCs were compared with matched primary and metastatic tumor tissues from the same patient. All major mutations observed in tumor tissues were identified in CTCs. Genetic analysis of CTCs offers diagnostic advantages such as high specificity and non-invasiveness for tumor mutation assessment and targeted therapy. The genetic characteristics of CTCs may reveal genotypic transition during tumor progression.

12:00 pm Close of Session

12:15 Luncheon Technology Workshop (Sponsorship Opportunity Available)

Transcription and the Single Cell

1:30 Chairperson’s RemarksJan Vijg, Ph.D., Professor and Chair, Genetics, Albert Einstein College of Medicine

» FEATuRED PRESENTATIoN1:35 Single-Cell TranscriptogenomicsJan Vijg, Ph.D., Professor and Chair, Genetics, Albert Einstein College of MedicineDuring organismal development and aging, changes in the genome of cells result in increased genetic mosaicism of the somatic tissues. To dissect this age-related intra-tissue heterogeneity, we developed single-cell, genome-wide sequencing procedures to measure both single nucleotide and structural variation. To directly link single-cell, genomic mutation loads to possible consequences at the level of the transcriptome, we then performed concurrent global mRNA amplification and whole-genome amplification of single cells followed by RNA-Seq and whole-exome sequencing, respectively. This method, “single-cell transcriptogenomics,” allows us to directly track the consequences of randomly induced genetic mutations on gene expression profiles in the same single cell.

2:05 Insights into the Regulation of Protein Abundance from Proteomic and Transcriptomic AnalysesChristine Vogel, Ph.D., Assistant Professor, Center for Genomics and Systems Biology, New York UniversityThe advent of large-scale sequencing and proteomics technologies has shown that translation and protein degradation regulation are as important as transcription to fine-tune cellular gene expression levels. We investigate general principles of protein expression regulation in eukaryotic cell systems, both under normal and stress conditions.

2:35 Sequencing the genomes and Transcriptomes of Single Human CellsAlec Chapman, Research Scientist, X. Sunney Xie Laboratory, Chemistry and Chemical Biology, Harvard UniversityWhile sequencing is rapidly revolutionizing the way biological questions are approached, the prevailing methods have been limited to studying large ensemble populations of cells, masking the heterogeneity that is crucial for understanding complex systems such as cancer and development. We have recently developed a technique—Multiple Annealing and Looping Based Amplification Cycles (MALBAC)—that is capable of uniform whole-genome amplification from single cells, achieving >90% coverage and enabling the detection of copy number variations and newly acquired single nucleotide variations with no false positives. Adapting MALBAC to transcriptome sequencing provides both improved technical reproducibility and increased sensitivity over existing methods and simultaneously

sequencing the genome and transcriptome from the same cell allows us to probe the relation between genotype and phenotype in heterogeneous populations.

3:05 Refreshment Break in the Exhibit Hall, Last Chance for Poster Viewing

3:35 you Need More Power: Designing Cost-Effective Experiments for Measuring Differential gene Expression using RNA-SeqMichele Busby, Ph.D., Computational Biologist, Broad Institute; former Research Scientist, Biology, Gabor T. Marth Laboratory, Boston CollegeRNA-Seq is a powerful tool for detecting differential gene expression, but only realizes its full potential when experiments are optimally designed. We will demonstrate how our computational tool Scotty can be used to design an experiment that contains an adequate number of samples sequenced to a sufficient depth to achieve experimental goals. We will further discuss how the performance of different RNA-Seq protocols can dramatically affect the power of an experiment and demonstrate computational techniques for assessing the performance of a protocol.

4:05 Deconvolution of Heterogeneous Tissue Samples Based on RNA-Seq DataTing Gong, Ph.D., Assistant Professor, Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterThe promising biomedical applications of NGS have spurred the development of new statistical methods to capitalize on the wealth of information contained in RNA-Seq datasets. However, for heterogeneous tissues, measurements of gene expression through RNA-Seq data can be confounded by the presence of multiple cell types present in each sample. Here, we present a statistical pipeline for deconvolution of heterogeneous tissues based on RNA-Seq data.

4:35 Panel Discussion with Afternoon SpeakersModerator: Jan Vijg, Ph.D., Professor and Chair, Genetics, Albert Einstein College of MedicinePanelists:Christine Vogel, Ph.D., Assistant Professor, Center for Genomics and Systems Biology, New York UniversityAlec Chapman, Research Scientist, X. Sunney Xie Laboratory, Chemistry and Chemical Biology, Harvard UniversityMichele Busby, Ph.D., Computational Biologist, Broad Institute; former Research Scientist, Biology, Gabor T. Marth Laboratory, Boston CollegeTing Gong, Ph.D., Assistant Professor, Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterAndrey Shabalin, Ph.D., Research Scientist, Edwin J.C.G. van den Oord Laboratory, Center for Biomarker Research and Personalized Medicine, Pharmacotherapy and Outcomes Science, Virginia Commonwealth UniversityChristina Schweikert, Ph.D., Division of Computer Science, Mathematics and Science, St. John’s University

5:00 Close of Single-Cell Sequencing Conference

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NGX Sequencing Data Analysis and Interpretation Progress in the Pipeline

August 20-21, 2013Sixth Annual

Sequencing a genome is only the beginning. Several layers of analysis are necessary to convert raw sequence data into an understanding of functional biology. First, error sources in the original raw data from multiple platforms and diverse applications must be accounted for. Then, as computational methods for assembly, alignment, and variation detection continue to advance, a broad range of genetic analysis applications including comparative genomics, high-throughput polymorphism detection, analysis of coding and non-coding RNAs, and identifying mutant genes in disease pathways can be addressed. CHI’s Sequencing Data Analysis and Interpretation conference combines unique perspectives from a variety of researchers, engineers, biostatisticians, and software developers involved in NGS data analysis.

TuESDAy, AuguST 20

12:00 pm Main Conference Registration


TuESDAy, AuguST 20



2:10 A Revolution in DNA Sequencing Technologies: Challenges and opportunitiesJeffery A. Schloss, Ph.D., Director, Division of Genome Sciences, National Human Genome Research Institute, National Institutes of HealthThe initial sequencing of the human genome spurred an appetite for much more human sequence information to better understand the contributions of human sequence variation to health and disease. However, despite dramatic reductions during the Human Genome Project,

the cost of sequencing was clearly too high to collect the very large numbers of human and numerous other organism genome sequences needed to achieve that understanding. In 2004, NHGRI launched parallel programs to reduce the cost of sequencing a mammalian genome initially by two (in five years), and eventually by four orders of magnitude (in ten years). This presentation will summarize the technologies that are in high-throughput use to produce stunning amounts of sequence and related data and novel biological insights, and will emphasize technologies currently emerging and on the horizon that may provide human genome sequence data with the nature, quality, cost and turnaround time needed for applications in research and medicine.

PRESENT YOUR RESEARCHGain further exposure by presenting your work in the poster sessions. To secure a poster board and inclusion in the conference materials, your abstract must be submitted, approved and your registration paid in full by July 12, 2013.

Reasons you should present your research poster at this conference:

• Your poster will be exposed to our international delegation.• Receive $50 off your registration.• Your poster abstract will be published in our conference materials.• Your research will be seen by leaders from top pharmaceutical, biotech,

academic and government institutes.

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5:35 Short Course Registration


WEDNESDAy, AuguST 21


Managing the Data Pipeline

8:45 Chairperson’s RemarksChris Dwan, Acting Senior Vice President, IT, New York Genome Center

FEATuRED PRESENTATIoN

8:50 Building the Next generation of Next-gen PipelinesToby Bloom, Ph.D., Deputy Scientific Director, Informatics, New York Genome CenterIn the early days of next-generation sequencing, the focus of informatics pipelines was on storing all the data, coping with network and compute bandwidth problems and reliably processing huge numbers of short reads. Seven years after that first Solexa instrument arrived, we now face a new set of daunting challenges: we must analyze larger and larger numbers of samples concurrently, combine many types of data in one analysis, identify and locate the needed data and integrate ever-larger amounts of clinical data. We discuss these challenges from both the perspective of the informatics infrastructure to support these analyses and the impact on the design on new methods and algorithms.

9:20 Can We Maintain Sanity as NgS Pipelines Change?Stuart M. Brown, Ph.D., Professor, Center for Health Informatics and Bioinformatics, New York University School of MedicineNGS technology and software are evolving very quickly. It is difficult to maintain a consistent analysis pipeline across an experiment or group of related experiments when samples are processed months or years apart. Sample preparation, sequencing technology and software can all influence the results, when the investigator is really only interested in the biology. Does the software alone have a substantial impact on the results reported for an RNA-seq experiment? We re-analyzed some FASTQ data files from experiments previously analyzed by the Illumina CASAVA RNA-seq pipeline and compared the results with alignments by TopHat and STAR and gene expression measured by Cufflinks.

9:50 SELECTED oRAL PoSTER PRESENTATIoN:Single-Cell RNA-Seq to Define Cell-Specific gene Expression In the Developing Lung Yan Xu, Ph.D., Associate Professor, Pediatrics, Division of Pulmonary Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati School of Medicine


11:00 Building a genomic Experiment Tracking and Analysis SystemCraig Pohl, Co-Director, Bioinformatics, The Genome Institute, Washington UniversityAs sequencing technology has become a commodity, The Genome Institute at Washington University has expanded from a large-scale sequencing center to a large-scale experimental genomics center. Our system currently tracks thousands of active projects, generating and analyzing their data automatically, where each project’s experimental design is customized according to the hypothesis in question. Therefore, our system seeks to address the fundamental problem of translating experimental inputs, such as sequence data and samples

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with rich metadata, into a highly efficient, cost effective, modular and automated genomic data analysis modeling system that provides customized results for each project. Insights gained from the process of developing this system will be shared.

11:30 Panel Discussion with Morning SpeakersModerator: Chris Dwan, Acting Senior Vice President, IT, New York Genome CenterPanelists:Toby Bloom, Ph.D., Deputy Scientific Director, Informatics, New York Genome CenterStuart M. Brown, Ph.D., Professor, Center for Health Informatics and Bioinformatics, New York University School of MedicineYan Xu, Ph.D., Associate Professor, Pediatrics, Division of Pulmonary Biology and Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati School of MedicineCraig Pohl, Co-Director, Bioinformatics, The Genome Institute, Washington University

12:00 pm Close of Session

12:15 Luncheon Technology Workshop (Sponsorship Opportunity Available)

Analysis and Interpretation

1:30 Chairperson’s RemarksMary Ann Brown, Executive Director, Conferences, Cambridge Healthtech Institute

1:35 Network Models: How to Make Sense of your NgS DataErnest Fraenkel, Ph.D., Associate Professor, Biological Engineering, Massachusetts Institute of TechnologyHow are we to make sense of the torrents of data from next-generation sequencing? In this talk, we will explain how network models provide biological insight into the data and generate testable hypotheses that are the key to understanding disease.

2:05 MBD-Seq and genotype-Methylation Association Study using Next-generation Sequencing TechnologiesAndrey Shabalin, Ph.D., Research Scientist, Edwin J.C.G. van den Oord Laboratory, Center for Biomarker Research and Personalized Medicine, Pharmacotherapy and Outcomes Science, Virginia Commonwealth UniversityVariation in DNA methylation has been repeatedly associated with a wide variety of human diseases. In this study, we aim to comprehensively characterize methylation quantitative trait loci (meQTLs) by associating genome-wide SNP genotypes with methylation measures across the methylome. The statistical and biological analyses of this study involve tests for association between each of over 5,000,000 SNPs and each of 4,954,484 CpG blocks. Our results indicate different mechanisms of local versus long-range genetic control of the methylome.

2:35 ChIP-Seq Analytics: Combining Multiple ChIP-Seq Peak Detection SystemsChristina Schweikert, Ph.D., Division of Computer Science, Mathematics and Science, St. John’s UniversityThe abundance of sequencing data being generated enables us to analyze genome-wide protein-DNA interactions, as well as evaluate and enhance computational and statistical techniques for locating protein binding sites. We define methods to merge and rescore

the regions of two peak detection systems and analyze the performance based on average precision and coverage of transcription start sites. The results indicate that ChIP-seq peak detection can be improved by applying score or rank combination. System combination and fusion analysis would provide a means to assess available technologies and assist researchers in choosing an appropriate system, and offer another approach to improve the performance of the ChIP-seq peak identification process.

3:05 Refreshment Break in the Exhibit Hall, Last Chance for Poster Viewing

3:35 you Need More Power: Designing Cost-Effective Experiments for Measuring Differential gene Expression using RNA-SeqMichele Busby, Ph.D., Computational Biologist, Broad Institute; former Research Scientist, Biology, Gabor T. Marth Laboratory, Boston CollegeRNA-Seq is a powerful tool for detecting differential gene expression, but only realizes its full potential when experiments are optimally designed. We will demonstrate how our computational tool Scotty can be used to design an experiment that contains an adequate number of samples sequenced to a sufficient depth to achieve experimental goals. We will further discuss how the performance of different RNA-Seq protocols can dramatically affect the power of an experiment and demonstrate computational techniques for assessing the performance of a protocol.

4:05 Deconvolution of Heterogeneous Tissue Samples Based on RNA-Seq DataTing Gong, Ph.D., Assistant Professor, Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterThe promising biomedical applications of NGS have spurred the development of new statistical methods to capitalize on the wealth of information contained in RNA-Seq datasets. However, for heterogeneous tissues, measurements of gene expression through RNA-Seq data can be confounded by the presence of multiple cell types present in each sample. Here, we present a statistical pipeline for deconvolution of heterogeneous tissues based on RNA-Seq data.

4:35 Panel Discussion with Afternoon SpeakersModerator: Jan Vijg, Ph.D., Professor and Chair, Genetics, Albert Einstein College of MedicinePanelists:Christine Vogel, Ph.D., Assistant Professor, Center for Genomics and Systems Biology, New York UniversityAlec Chapman, Research Scientist, X. Sunney Xie Laboratory, Chemistry and Chemical Biology, Harvard UniversityMichele Busby, Ph.D., Computational Biologist, Broad Institute; former Research Scientist, Biology, Gabor T. Marth Laboratory, Boston CollegeTing Gong, Ph.D., Assistant Professor, Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterAndrey Shabalin, Ph.D., Research Scientist, Edwin J.C.G. van den Oord Laboratory, Center for Biomarker Research and Personalized Medicine, Pharmacotherapy and Outcomes Science, Virginia Commonwealth UniversityChristina Schweikert, Ph.D., Division of Computer Science, Mathematics and Science, St. John’s University

5:00 Close of Sequencing Data Analysis and Interpretation Conference

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Sponsorship, Exhibit, & Lead Generation OpportunitiesCHI offers comprehensive sponsorship packages which include presentation opportunities, exhibit space and branding, as well as the use of the pre and post-show delegate lists. Customizable sponsorship packages allow you to achieve your objectives before, during, and long after the event. Signing on early will allow you to maximize exposure to hard-to-reach decision makers

Agenda PresentationsShowcase your solutions to a guaranteed, highly-targeted audience. Package includes a 15 or 30-minute podium presentation within the scientific agenda, exhibit space, on-site branding and access to cooperative marketing efforts by CHI.

Breakfast & Luncheon PresentationsOpportunity includes a 30-minute podium presentation. Boxed lunches are delivered into the main session room, which guarantees audience attendance and participation. A limited number of presentations are available for sponsorship and they will sell out quickly. Sign on early to secure your talk!

Invitation-Only VIP Dinner/Hospitality SuiteSponsors will select their top prospects from the conference pre-registration list for an evening of networking at the hotel or at a choice local venue. CHI will extend invitations and deliver prospects. Evening will be customized according to sponsor’s objectives i.e.:

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ExhibitExhibitors will enjoy facilitated networking opportunities with high-level conference delegates. Speak face-to-face with prospective clients and showcase your latest product, service, or solution.

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Conference Hotel:Omni Providence HotelOne West Exchange StreetProvidence, RI 02903Phone: 401-598-8000 Discounted Room Rate: $165 s/dDiscounted Reseveration Cut-off Date: July 19, 2013Please visit our conference website to make your reservation online or you may call the hotel directly. You will need to identify yourself as a Cambridge Healthtech Institute conference attendee to receive the discounted room rate with the host hotel. Reservations made after the cut-off date or after the group room block has been filled (whichever comes first) will be accepted on a space and rate-availability basis. Rooms are limited, so please book early.

Why Stay at the Omni Providence?

The Omni Providence was awarded the prestigious “Highest in Hotel Guest Satisfaction among Upper-Upscale Hotel Chains” award by JD Power and Associates for 2012. In addition to being attached to the upscale Providence Place Mall, it is within walking distance to some of the city’s best historic attractions, gourmet restaurants, shopping and entertainment. The hotel features an indoor pool and complimentary wireless internet in all guest rooms.

We realize you have many choices when making your travel arrangements. Please understand that reserving your room in the CHI room block at the conference hotel allows you to take full advantage of the conference sessions, events and networking opportunities, and ensures that our staff will be available to help should you have any issues with your accommodations.

Flight Discounts:

Special discounts have been established with American Airlines for this conference.• Call American Airlines 1-800-433-1790 and use Conference code 8283BJ.• Go online www.aa.com/group and enter Conference code 8283BJ in promotion discount box.• Contact our dedicated travel agent Rona Meizler at 1-617-559-3735 or

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Car Rental Discounts:Special discounts have been established with Hertz for this conference. Please use one of the following methods:• Call Hertz 1-800-654-3131 and use our Hertz Convention Number (CV): 04KL0004.• Go online www.hertz.com and use our Hertz Convention Number (CV): 04KL0004.

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ADDITIoNAL REgISTRATIoN DETAILSEach registration includes all conference sessions, posters and exhibits, food functions, and access to the conference proceedings link.Handicapped Equal Access: In accordance with the ADA, Cambridge Healthtech Institute is pleased to arrange special accommodations for attendees with special needs. All requests for such assistance must be submitted in writing to CHI at least 30 days prior to the start of the meeting.To view our Substitutions/Cancellations Policy, go to http://www.healthtech.com/regdetailsVideo and or audio recording of any kind is prohibited onsite at all CHI events.

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SHoRT CouRSES Commercial Academic, government, Hospital-affiliated

One short course $695 $395Two short courses $995 $695

Monday, August 19 Tuesday, August 20SC1: Mapping Genomes in 3D SC3: Assembly and Alignment

SC2: Sample Prep SC4: Cancer Genetics and Epigenetics

CoNFERENCE PRICINgBASIC PACKAgE (Includes access to 1 conference, excludes short courses)

Advance Registration Discount until July 12, 2013 $1495 $695Registrations after July 12, 2013, and on-site $1745 $775

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Advance Registration Discount until July 12, 2013 $2145 $1045Registrations after July 12, 2013, and on-site $2345 $1095

August 19-20, 2013 August 20-21, 2013Sequencing Strategies for Success Single-Cell Sequencing

Dynamics of the Microbiome on Health and Disease Sequencing Data Analysis and Interpretation

CoNFERENCE DISCouNTS

Poster Submission – Discount ($50 off)Poster abstracts are due by July 12, 2013. Once your registration has been fully processed, we will send an email containing a unique link allowing you to submit your poster abstract. If you do not receive your link within 5 business days, please contact [email protected]. *CHI reserves the right to publish your poster title and abstract in various marketing materials and products.

Alumni Discount SAVE 20%: We appreciate your past participation at our events. Through loyalty like yours, this event has become a must-attend for senior level decision makers. As a result of your great loyalty, we are pleased to extend this exclusive opportunity to save an additional 20% off the registration rate. Simply select the “Alumni Discount” option on the online registration form to take advantage of this special offer.

NgS Leaders Discounts: Members of the NGS Leaders community will receive a $50 discount off the conference registration.

REgISTER 3 - 4th IS FREE: Individuals must register for the same conference or conference combination and submit completed registration form together for discount to apply. Please reproduce this registration form as needed.

group Discounts are Available! Special rates are available for multiple attendees from the same organization. For more information on group discounts contact David Cunningham at 781-972-5472.*Alumni, NGS Leaders, Twitter, LinkedIn, Facebook or any other promotional discounts cannot be combined. Discounts not applicable on Event Short Courses.

If you are unable to attend but would like to purchase the NGX Applying Next-Generation Sequencing CD for $750 (plus shipping), please visit Healthtech.com/sequencing. Massachusetts delivery will include sales tax.

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