TUESDAY, SEPTEMBER 23
8:00 Java and Jive Break-out Discussion Groups
Time has been designated for facilitated discussion groups with specific themes. This unique opportunity allows conference participants to focus on a topic and exchange ideas, information, experiences, and develop future collaborations.
IT’S ALL IN THE RNA
9:00 Chairperson’s Remarks
9:05 MicroRNA and Pre-microRNA Profiles as Ascertained by Automated Real-Time QPCR Arrays Contribute Non-Redundant Information to Tumor Classification
Dirk P. Dittmer, Ph.D., Associate Professor, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
MicroRNA signatures are useful classifiers of disease, e.g. lymphoma. Each microRNA is derived from a nuclear pre-cursor, which so far has been underutilized for tumor profiling. We developed a high-throughput real-time QPCR approach to pre-microRNA profiling, which allows us to simultaneously profile pre- and mature microRNAs from routine (2x2 mm) clinical biopsies. Validation and application of this approach to the classification of viral lymphoma will be discussed.
9:35 ExpressSeq Pipeline: Gene Expression Analysis using Next Generation Sequencing Technologies
Roderick Jensen, Ph.D., Director, Core Laboratory Facility, Virginia Bioinformatics Institute
With the falling prices and expanded throughput of the next-generation sequencing platforms, these instruments will soon be competing with the DNA microarray technologies for global gene expression analysis. To provide a preliminary evaluation of the performance of these promising technologies, we performed deep sequencing of the Microarray Quality Control (MAQC) reference RNA samples using the Roche/454 GS-FLX. For this study we generated more that 3.6 million sequence reads of average length 250 Bp for cDNA generated from the MAQC A and B samples and introduced the “ExpressSeq” Pipeline for translating the cDNA read counts into gene expression levels. Using the metrics for evaluating the performance of gene expression platforms used in the MAQC studies, we found that the ExpressSeq results for gene expression levels showed excellent specificity, good sensitivity and reproducibility that improved systematically with increasing sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRT-PCR results. Moreover, in addition to gene expression levels, the ExpressSeq results also provide useful information about splice variants, gene fusions, and single nucleotide polymorphisms (eSNPs) in expressed genes.
10:05 Technology Spotlight Sponsored by
The NanoString nCounter System: A Highly Sensitive, Digital Technology for Multiplexed Measurement of Gene Expression Without Reverse Transcription or PCR
Sean Ferree, Ph.D., Research & Development Manager, NanoString Technologies
We describe a novel technology, the NanoString nCounter Analysis System, that captures and counts individual mRNA transcripts. Advantages over existing platforms include direct measurement of mRNA expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.9999, a detection limit between 0.1fM and 0.5fM, and a linear 1000-fold dynamic range. Comparison of the NanoString nCounter gene expression system with microarrays and RT-PCR, demonstrated that the nCounter system is significantly more sensitive than microarrays and very similar in sensitivity to RT-PCR. Finally, a comparison of transcript levels for 21 genes across 7 samples measured using both the nCounter system and quantitative RT-PCR demonstrated a remarkable correlation in the pattern of gene expression at all transcript levels.
10:20 Morning Coffee, Poster and Exhibit Viewing
11:00 External RNA Control Consortium Reference Material: Community Built Measurement Assurance Tools
Marc Salit, Ph.D., Research Chemist, Team Leader, Metrology for Gene Expression, NIST
Gene expression microarrays are a rapidly maturing technology, and the community has come together and developed tools and methods to assure measurement quality. NIST has played host to this consortium, and it has been a key element in our effort to evaluate a systematic approach toward genome-scale measurement assurance. Our program at NIST is creating a plasmid library of reference material to be used for manufacture of the external RNA controls, and is investigating methods for using them to validate the technical performance of expression microarrays and qRT-PCR. The results of the ERCC testing, and the status of the reference material development will also be presented.
11:30 Panel Discussion with Morning Speakers
12:00 pm Close of Session
12:15 Luncheon Technology Workshop
Sponsored by
A Novel Method for High-Throughput, Nanoliter Volume Real-Time PCR
Kevin Munnelly M.B.A., Vice President and General Manager, BioTrove
Understanding patterns of gene expression and gene function requires accurate and precise measurement of RNA levels across large numbers of genes simultaneously. This talk will demonstrate a novel, highly parallel, nanofluidic system capable of performing approx. 3000 real-time polymerase chain reactions based on standard chemistries. The utility of this system for studying various gene expression applications as well as pathogen detection and methylation-specific PCR will be shown. The session will focus on the following:
- Motivations for the development of this high throughput nanoliter system.
- The technical design and uses of the system.
- Performance data
- Applications for genomic research
TECH EXPO
Explore available next-generation screening platforms as presented by sequencing leaders. An unparalleled opportunity to compare and contrast these next-generation sequencing platforms to best suit your research needs.
Sponsored Seminar Hosted by:
2:00 Chairperson's Remarks
Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
2:05 Sponsored By
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The SOLiD System - Setting New Standards in Genomic Analysis
Michael Rhodes, Ph.D., Product Applications Senior Manager, Genetic Analysis, High Throughput Discovery, Applied Biosystems
The SOLiD™ System generates in excess of 6Gb of mate paired sequence data from a single run and recent throughput in the range of 12-17Gb has been demonstrated in Applied Biosystems R&D labs as well as customer sites. This enables the rapid sequencing of entire human genomes. As a result of this data availability, Applied Biosystems has sequenced a single Yoruban and analyzed the data for SNPs, insertions and deletions and structural variations. This presentation will review some of the challenges of analyzing such data sets. The advantages di base encoding will be discussed, especially in context of SNP calling. In addition, the use of Mate pairs and the latest tools for utilizing SOLiD™ System data will be presented.
2:35 Sponsored by
True Single Molecule Sequencing™: The Continuing Path to the $1000 Genome
Patrice M. Milos, Ph.D., Vice President and Chief Scientific Officer
The Heliscope™ Single Molecule Sequencer, an advanced technology platform capable of directly measuring single DNA molecules without the cost and complexity of amplification, provides the opportunity for high throughput genomic studies to address important biological questions. This presentation will provide an update on the platform as well as describe scientific applications that are being developed for the platform including recent studies on genomic sequencing, SNP detection, expression studies, and paired reads.
3:20 Refreshment Break, Poster and Exhibit Viewing
4:00 Sponsored by
Length Really Matters: 400 Base Pair Sequencing Reads Using the 454 Genome Sequencer FLX
Jason Affourtit, Director of Advanced Technologies
With over 250 publications, the Genome Sequencer FLX system has been demonstrated to support an increasing number of applications from whole genome shotgun sequencing to the detection of somatic mutations. Recent advancements in the technology allow for the generation of over 1 million sequencing reads that are between 400 to 500 base pairs in length, allowing for the displacement of traditional Sanger sequencing technologies. The addition of paired end sequencing with spacing of 20kb between the sequencing tags has enabled whole genome sequencing of complex genomes. Data will be presented showing the de novo assembly of Arabidopsis and drosophila. Additional examples of cDNA, metagenomics, and amplicon studies will be shown.
4:30 Sponsored by
Enabling Genome Biology with the Illumina Genome Analyzer
Gary P. Schroth, Ph.D., Senior Director, Applications R&D
The Illumina Genome Analyzer is an ultrs-high throughput DNA sequencing platform that routinely generates billions of bases of very high quality sequence information from each short run. We will show examples of how the instrument is being used for a large variety of applications in genome biology including human genome sequencing, SNP discovery, gene expression analysis, protein-DNA interactions (ChIP-seq), genome-wide DNA methylation analysis, and small RNA discovery and profiling. We will discuss the development of software and analysis tools that can help users glean biological meaning from the massive amounts of data produced by the system.
5:00 Interactive Panel Discussion
Moderator, Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
It’s been three years since the debut of the first commercial next-generation sequencing platform. Since then, remarkable advances have been made in the quality, reliability, and throughput of all of the major commercial platforms. This session features presentations from some of the most established next-gen platform providers, showcasing advances in technology, affordability, and applications.
6:00 Close of Meeting
6:30-8:30 Recommended Short Course III or IV * (Separate Registration Required)