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Please click here to download the following podcasts: 

In the Wake of the Flood 

Taking NGS into the Clinic 

1000 Genomes Project: Cancer, Genetic Variation, and Drug Response 

Mapping Genomes in 3D 

The Human Microbiome Project: Next-Generation Sequencing and Analysis of the Indigenous Microbiota 

Building a Genome Sequencing Center: Managing and Mining Two Years of NGS Data 


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Tuesday, September 27



Sponsored byGenomatix Software 7:30 am Breakfast Presentation
Results Matter: Examples of NGS Data Interpretation in Personalized Medicine 
Martin Seifert, Ph.D., CEO, Genomatix Software & Thomas Langmann, Ph.D., Professor, University Hospital RegensburgPersonalized Medicine aims to provide medical treatment specific to an individual's genomic makeup. A biologically intelligent interpretation of genomic NGS data is critical to this process. The presentation is split into two sections, a general introduction and application examples of medically meaningful results obtained from NGS data.

8:15 Successful Sequencing Discussion Groups

Grab a cup of coffee and join a facilitated discussion group focused around specific themes. This unique session allows conference participants to exchange ideas, experiences, and develop future collaborations.

Challenges of Detecting Structural Variants in Tumor Samples
Martina Mijuskovic, Ph.D., Postdoctoral Associate, Center for Health Informatics and Bioinformatics, New York University Langone Medical CenterDiscussion topics include:
• Mate pair vs. paired end sequencing: Which method to use?
• How to predict necessary coverage: effect of repetitive genomic sequences, effect of tumor heterogeneity
• Experiences with different structural variant calling algorithms

NGS Technology AssessmentDavid I. Smith, Ph.D., Professor, Laboratory Medicine and Pathology, Mayo ClinicDiscussion topics include:
• Evaluate advances in sequencing technology, including molecular sequencers
• Discuss supportive technologies such as capture and robotics to make libraries

Alleviating the NGS Bottlenecks Created by Sample PreparationSteven R. Kain, Ph.D., Director, Product Marketing, NuGEN Technologies, Inc.Discussion topics include:
• What are the bottlenecks limiting your ability to process more samples by NGS?
• How significant is the challenge of working with different sequencing platforms?
• How important is it to standardize protocols?
• Is automation the answer?

Handling the Opportunities and Challenges of Diverse Platforms and Projects in a Core EnvironmentMichael W. Smith, Ph.D., Vice President, Director, Genetics and Genomics Group, Advanced Technology Program, SAIC-Frederick, National Cancer Institute at FrederickDiscussion topics include:
• Overview of current NGS platforms experience
• Finding suitable projects
• Matching projects to platforms
• Managing investigator expectations

Using Next-Gen Sequencing for Genome Wide Association Studies (GWAS)Stephanie Costello, Director of Sales, Distribution and Technical Support, DNASTAR Discussion topics include:
• Benefits of using sequencing
• How to analyze the data?
• SNPs and other structural variations
• Integration of existing data (previous studies and databases)

NGS Data Analysis and Medical Applications: From Data to Results – How Much Is Enough?Peter Grant, CEO, Genomatix Software, Inc.Discussion topics include:
• How much Information is provided by genomic variants?
• How do we extract biological/medical KNOWLEDGE from this information?
• What are the building blocks needed to build the road to medically relevant knowledge?

QA and QC During Secondary Analysis:  What are You Doing Now and What Do You Wish Software Could Do for You?
Jean Jasinski, Ph.D., Field Application Scientist, Partek, Inc.Discussion topics include:
• What parameters do you examine before aligning reads to the reference? 
• What parameters do you examine after alignment?
• Which operations should be used to deal with poor quality reads (filter, trim, remove, repair, etc.)?
• If you had a programmer in your pocket, which features would you request?

Using Whole Genomes and Exomes for Drug DevelopmentNathan Pearson, Director of Research, Knome, Inc.Discussion topics include:
• What phase(s) of drug development can benefit most from comprehensive sequence analysis? 
• In-house or outsource analysis?
• Can we understand efficacy?  Dosage?  Adverse events?

Open-Source Versus Commercial SoftwareHarsha Rajasimha, Ph.D., Consultant, Bioinformatics and Next-Generation Sequencing, NIHDiscussion topics include:
• Where do you see the field of NGS software going… toward open-source, commercial, or in-between?
• How would the NGS software look differently 3-5 years from now (web-based, cloud-based or desktop workbenches

Sequencing from Personal Genomics to Personalized Medicine 

9:15 Chairperson's Remarks

Thomas Langmann, Ph.D., Professor, University Hospital Regensburg

9:20 Impact of Next-Generation Sequencing in Biomarker Assessment

Brian Dougherty, Principal Scientist, Molecular Science, Amgen, Inc.

The talk will cover the next-generation sequencing technology based on 454 platform that has been employed to assess mutation status of multiple gene loci in archival patient tumor samples from a randomized clinical trials. The ability to determine the somatic mutation status of DNA extracted from FFPE samples at high sensitivity enabled its use to identify gene mutations beyond KRAS for evaluation of response to for panitumumab in a randomized, phase 3, in monotherapy study of metastatic colorectal cancer (mCRC).

9:50 Gene Inactivation and Its Implications for Annotation in the Era of Personal Genomics

Suganthi Balasubramanian, Ph.D., Associate Research Scientist, Molecular Biophysics and Biochemistry, Yale University

With the advent of next-generation sequencing genomes, whole genome sequencing of personal genomes is becoming routine. This rapid progress has enabled us to discover that no single individual genome contains the full complement of functional genes. We highlight the inadequacy of the current reference genome and present a proposal to define a reference gene set that will remain stable as more individuals are sequenced. We also call for a revised definition of a reference genome in light of the enormous variations that we are discovering between individuals.

Sponsored by
Beckman Coulter
10:20 High Throughput Sample Prep for Next Generation Sequencing Labs - 96 Libraries in under 6 Hours

Brian Komorous, Product Manager, Beckman Coulter GenomicsBeckman Coulter's SPRIworks HT sample preparation solution provides automated library construction for 8-96 samples with flexible built in size selection. By combining SPRI reagents and Biomek automation, we have developed a fully supported solution for Illumina sequencing sample prep. Data shown will highlight the capabilities of the SPRIworks HT system.

10:35 Networking Coffee Break in the Exhibit Hall with Poster Viewing

11:15 From Personal Genomes to Actionable Diagnostics

Patrick Terry, Partner, Pricing, Reimbursement & Market Access, Scientia Advisors LLC

The complex conceptual, logistical and medical delivery challenges of translating massive data sets into actionable and commercially viable diagnostics products continues to perplex the entire enterprise of Next-Gen Sequencing. The opportunities to potentially introduce profound new information and novel clinical insight to patients and physicians is very compelling but the technical and legacy systems of health care delivery can counter balance these opportunities with significant road blocks. This talk will address some of these road block issues and share potential ways to navigate around the short term obstacles while at the same time managing for the future of optimized molecular diagnostics and personalized medicine.

11:45 Panel Discussion with Speakers 

12:15 pm Close of Session


Sponsored by
PerkinElmer NEW 2009 
12:30 pm Luncheon Presentation
Data Analysis for Next Generation Sequencing: Challenges and Solutions

N. Eric Olson, Ph.D., Senior Leader, Product Development, GeospizaThe presentation will include an overview of Whole Transcriptome Sequencing, Small RNA sequencing and Exome Resequencing and the specific data analysis needs and challenges for each application. Topics covered will include Secondary Analysis (alignments, gene models, etc.) as well as Tertiary Analysis (multi-sample comparisons, biological annotation, etc.) for each application. Geospiza's cloud-based GeneSifter Analysis Edition software will be used to present best-practice analysis workflows using sample data sets from NCBI's GEO and SRA.

Transcription – Insights into the Active Genome 

2:00 Chairperson's Remarks

David I. Smith, Ph.D., Professor, Laboratory Medicine and Pathology, Mayo Clinic


2:05 ChIP-exo: A Technique to Map a Complete Set of Genomic Protein-DNA Interactions at Single Base AccuracyHo Sung Rhee, Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityChromatin immunoprecipitation (ChIP) is commonly used to locate where proteins bind throughout a genome. However, due to DNA contamination and DNA fragmentation heterogeneity, ChIP cannot identify a complete and exact set of genomic locations. Here we report a novel strategy, ChIP-exo, that takes advantage of lambda exonuclease's ability to digest DNA in a 5' to 3' direction, followed by deep sequencing. We report a nearly complete set of in vivo binding locations, and accurate to within 1 bp, for tested samples from yeast to humans, and reveal diverse rules governing in vivo DNA binding specificity.

2:35 Effects of Nickel Treatment on H3K4 Trimethylation and Gene Expression

Hong Sun, Ph.D., Assistant Professor, Environmental Medicine, NYU School of Medicine


Sponsored by
3:05 Transcriptome Profiling Solutions for Eukaryotes and Prokaryotes

Steve Kain, Ph.D., Director, Product Management, NuGEN Technologies

Advances in Next-Generation Sequencing (NGS) have increased both the throughput and capacity of sequencing platforms, calling for increased efficiency in cDNA preparation and the ability to work with small, degraded, and heterogeneous samples. NuGEN's portfolio of NGS products meets this challenge by enabling simple, rapid and affordable workflows with a broad range of sample types. Data will be presented for RNA-Seq studies in diverse areas of research such as oncology, viral assembly, immunology and metagenomics with the common thread of enabling studies with the most precious RNA samples.

3:20 Networking Refreshment Break in the Exhibit Hall with Poster Viewing

Sponsored by
DNA Star
4:15 Methodology and Analysis Workflow for Next-Generation Population Genomics without a Reference Genome

Thomas L. Parchman, Post Doctoral Scientist, University of Wyoming

Genomic reduction and highly multiplexed sequencing now allow population genomic data to be readily generated for nearly any organism. I will describe a simple method to generate such data and a workflow for assembly, parsing and analysis.

4:45 Highly Consistent, Fully Representative mRNA-Seq Libraries from Ten Nanograms of Total RNA

Srikumar Sengupta, Ph.D., Assistant Scientist, Regenerative Biology Laboratory, Morgridge Institute for Research

We describe an Illumina mRNA-Seq library preparation protocol based on T7 linear RNA amplification that requires only 10 ng total RNA as starting material. This protocol does not introduce significant bias and generates a directional library that represents the whole-transcript and is highly consistent across over three orders of magnitude of input RNA.

5:15 RNA-Seq Based Monitoring of Infection-Linked Changes in Vibrio cholerae Gene Expression
Anjali Mandlik, Ph.D., Research Fellow, HHMI, Brigham and Women's Hospital
High-throughput cDNA sequencing (RNA-seq) was used to quantitatively catalog the transcriptome of the cholera pathogen during infection of two model hosts and when bacteria were grown in lab media. Especially when coupled with analyses of metabolites present in cecal fluid from infected rabbits, the RNA-seq data yielded insights into the bacteria's environment within the host and into the mechanisms that control pathogen gene expression.  RNA-seq-based analysis of a pathogen's transcriptome during infection produces a robust, sensitive, and accessible data set for evaluation of regulatory responses driving pathogenesis.

5:45 Close of Day

Sponsored byPartek New 6:00-9:00 Dinner Short Course Three: Start-to-Finish Analysis of a Multi-Assay Next Generation Sequencing StudyInstructors:
Jean Jasinski, Ph.D., Field Application Scientist, Partek
Ryan Peters, M.Sc., Field Application Specialist, Partek

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