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Exploring Next Generation Sequencing - Day 2

Conference Proceeding CD Now Available
  • Speaker Presentations
  • Poster Abstracts
  • and More!



8:15 am Morning Coffee

8:30 Chairperson’s Remarks
Michael Rhodes, Ph.D., Product Applications Senior Manager, Applied Biosystems

Massively Parallel High Throughput DNA Sequencing: Automation for Microbial Community, Gene Expression and de Novo Deciphering of New Genomes
Bruce A. Roe, Ph.D., George Lynn Cross Research Professor of Chemistry and Biochemistry, Advanced Center for Genome Technology, Stephenson Research and Technology Center, University of Oklahoma
This presentation discusses the modifications Dr. Roe’s laboratory has introduced to streamline the up-front sample preparation protocols, to improve sample read length and to automate the library and sample preparation steps prior to DNA sequencing.   The results obtained from applying these techniques to study microbial communities, eukaryotic gene expression and the de novo sequencing of new genomes will be discussed and compared to those obtained using more classical approaches.

Setting Up a Next-Generation Sequencing Lab Sequencing Center Insights

9:20 Beijing Genomics Institute
Sequencing more Human Genomes by the Next-Generation Technology
Laurie Goodman,  Ph.D., Goodman Writing and Editing
New sequencing technologies are in the process of reducing the cost of sequencing by two orders of magnitude. This means that we can now begin to characterize the full distribution of human genome sequences across mankind directly, observing all the variation in the sequence of multiple individuals by sequencing them. Taking advantage of such development, this project is aiming at sequencing more Chinese individuals and creating a genetic variation map.

9:45 Broad Institute
Feeding the Beasts: High Throughput Sample Preparation for Next Generation Sequencing Platforms

Andrew Barry, Supervisor, Genome Sequencing Platform
Next-generation sequencing platforms produce unparalleled quantities of data at a low cost.  As these technologies mature, novel applications for sequence analysis include de novo assembly, variant detection, metagenomic, and epigenomic analyses.  With falling costs, higher throughput, and a growing number of applications, the quantity of samples requiring sequence data has exponentially increased.  In order to meet this demand, alternative methods to prepare, track, and interrogate samples prior to sequencing are rapidly being developed.  My talk will focus on the methods developed at the Broad Institute to create a high-throughput sample preparation pipeline for use upstream of next-generation sequencing.

10:10 Morning Coffee, Poster and Exhibit Viewing

11:00 J. Craig Venter Institute (JCVI)
Transitioning into the “Next-Generation” Sequencing Technologies
Yu-Hui Rogers, Vice President, Core Technology Development and Services
The presentation will discuss JCVI’s experiences in validating, implementing and scaling up the next-generation sequencing technologies and the challenges we face in managing a high throughput sequencing facility with multiple sequencing platforms.  Examples of how the next-generation sequencing technologies are being applied at JCVI to support various research programs will also be discussed.

11:25 Washington University
The Whirlwind of Next-Generation Implementation
Vincent Magrini, Ph.D., Technology Development Research Faculty, Genetics Sequencing Center 
Current platforms in use include both the 454 FLX and Titanium (XLR) instruments, the Illumina Genome Analyzer (GA) and upgraded GAII instruments, as well as the AB SOLiD platform.  Thus, we are in a whirlwind of upgrades, modifications, and technologies all aimed at generating large volumes of high quality sequence data.  Here, we will highlight platform specific applications, upgrades, and performance.

11:50 Close of Session

12:00 Luncheon Technology Workshop  Sponsored by agilent logo
Focusing the Next-Generation Sequencing Workflow:  Agilent’s New Targeted Re-Sequencing Sample Preparation Platform
Carsten Russ, Ph.D., Research Scientist, Genome Sequencing & Analysis Program, Broad Institute of MIT & Harvard
Remarkable technological advances have been made enabling scientists to examine genetic diversity more efficiently. Next-generation sequencing technology has introduced the ability to sequence DNA in a massively parallel manner, but with this improvement in throughput has come the need to easily target specific regions of genomes under study. Agilent Technologies has leveraged its ability to efficiently manufacture high fidelity long oligonucleotides to develop the Agilent Technologies Targeted Re-Sequencing Platform, a set of sample-preparation products to enable next-gen users to sequence just what they want and discard the rest, significantly increasing the cost efficiency of these platforms. This presentation will demonstrate the following benefits of these new products: Increased sequencing efficiency – targeting genomic areas of interest; Single tube processing – ease of use in a highly scalable and automatable format; Solution-based kinetics – extremely low input DNA required compared to alternative methods.

Setting Up a Next-Generation Sequencing Lab Core Facility Experiences

2:00 Chairperson’s Remarks
Yu-Hui Rogers, Vice President, Core Technology Development and Services

2:05 University of Washington
Bacterial Genomic Sequencing of Several Strains of Actinobacillus Actinmycetocomitans (Aa) an Oral Bacterium
Roger Bumgarner, Associate Professor, Microbiology
In collaboration with Dr. Casey Chen in the USC School of Dentistry, we have been sequencing a number of strains of Aa and performing comparative genomics analyses.  To date, we have sequenced a total of seven strains and many more are in progress.  Our results show a surprising amount of genomic rearrangement between different strains of the same species.  In addition, we are characterizing the complete set of genes associated with this species.  While each individual genome contains about 2600 unique genes, the unique gene content of all seven strains is well over 5000 genes.  These results have important implications for both the concept of and the utility of a “reference genome” for bacteria.

2:30 Cornell University
The Agony and the Ecstasy: Implementation of Next-Generation Sequencing Technologies as Core Facility Resources

George Grills, Ph.D., Director of Operations, Core Facilities in the Life Sciences; Director, Advanced Technology Assessment, Life Sciences Core Laboratories Center
The Cornell University Life Sciences Core Laboratories Center has implemented next-generation sequencing platforms as academic core facility shared research resources.  We have established sample handling methods and informatics tools to build robust processing pipelines in support of these new technologies.  Our DNA sequencing and genotyping core laboratory provides sample preparation and data generation services and in collaboration with the gene expression and informatics core facilities, provides both project consultation and analysis support for a wide range of applications, including whole genome assembly, amplicon resequencing, mutation detection, SNP genotyping, small RNA profiling, and genome-wide measurements of protein-nucleic interactions.  Implementation of next-generation sequencing platforms as shared resources with multi-disciplinary core facility support enables cost effective access and broad based use of these emerging technologies. 

2:55 University of Florida
Implementing Next-Gen DNA Sequencing Services at the University of Florida
Savita Shanker, Ph.D., Assistant Scientist, Interdisciplinary Center for Biotechnology Research
The University of Florida Interdisciplinary Center for Biotechnology Research (ICBR) will report on their experience implementing 454 DNA sequencing technology. The cost efficiency and production capacity of nextGen DNA sequencers opens novel research opportunities having wide-ranging applications. As an early adopter of the 454 DNA sequencing platform, ICBR had several primary considerations such as funding, dedicated space, impact on Sanger sequencing operations, technical expertise, and data delivery.  In addition, some of their early experiences with the SOLiD DNA sequencer, an ABI platform, will be presented.

3:20 Refreshment Break, Last Chance for Poster and Exhibit Viewing

4:00 McGill University
Massively Parallel Sequencing
Ken Dewar, Ph.D., Associate Professor, Department of Human Genetics, McGill University and Genome Quebec Innovation Centre 
The McGill University and Genome Quebec Innovation Centre is using massively parallel sequencing technologies for comparative microbial genomics, human regional resequencing, gene expression, and metagenomics.  Sequencing projects are managed through our internal LIMS system using a Roche GS-FLX and results are accessible to clients on our password protected website.  Data analysis is supported by an integration with resources including the UCSC genome browser.

4:25 Interactive Panel Discussion with the Days Speakers
Moderator, Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World
Deploying next-generation instrumentation in centralized or core facilities brings with it a host of potential issues, from maximizing throughput to handling data to integration of different platforms. In this interactive panel discussion, experts from a number of leading institutions share their “hands on” experiences in deploying next-gen platforms and realizing their full potential.

5:30 Close of Day

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