WEDNESDAY, SEPTEMBER 23, 2009
7:30am Breakfast Presentation Sponsored by 
Enrichment of Genomic Loci for Targeted Sequencing Applications
James Brayer, Manager of Commercial Scientific Applications, RainDance Technologies
RainDance Technologies has developed a platform to enable the use of PCR for high-throughput amplification of targeted genomic sequences. The Sequence Enrichment application manipulates picoliter volume droplets in disposable microfluidic chips. RainDance will describe the use of this novel method for enrichment of genomic loci with minimal selection bias prior to sequencing, demonstrating the utility of this approach for the routine application of targeted sequencing.
SEQUENCING APPLICATIONS
8:15 Chairperson’s Remarks
Michael Rhodes, Ph.D., Sr. Manager, Applied Biosystems
8:20 Targeted Sequencing of Human Genomes, Transcriptomes and Methylomes
Jin Billy Li, Ph.D., Research Fellow, Genetics, Harvard Medical School
Next-generation sequencing technologies have significantly lowered the cost of DNA sequencing. However, it is still prohibitively costly to sequence the full human genomes, transcriptomes, and methylomes. Specifically capturing and amplifying genomic regions of interest in parallel enables us to fully utilize the power of new sequencing technologies. We developed a padlock-based approach to amplify 55,000 exons in a single reaction and have continuously improved the capturing efficiency by ~10,000-fold. In addition to specific capturing of genomic features such as exons, simultaneous targeting of the same sites in both genomic DNA and cDNA allowed us to identify allele-specific gene expression patterns and hundreds of novel A-to-I RNA editing sites. Because of the near 100% specificity of the padlock approach, we extended our technology to bisulfite converted human genomic DNA. Despite the lowered genomic complexity, we were also able to accurately measure cytosine methylation level at 10,000 CpG loci in a single capturing and sequencing reaction. Interesting biological discoveries will also be discussed.
8:50 The Structure and Complexity of a Bacterial Transcriptome
Nicholas Bergman, Ph.D., Assistant Professor, Biology, Georgia Institute of Technology
We have recently used a high-throughput sequencing-based approach (RNA-Seq) to assemble the first comprehensive, single-nucleotide resolution view of a bacterial transcriptome. We sampled the Bacillus anthracis transcriptome under a variety of growth conditions, and showed that our data provide an accurate and high-resolution map of transcript start sites and operon structure throughout the genome. Further, the data identified previously unannotated regions with significant transcriptional activity, and enhanced the accuracy of existing genome annotations. Finally, our data provide estimates of absolute transcript abundance, and provide a glimpse of the transcriptional heterogeneity that exists within a clonal, synchronized bacterial population.
9:20 High Throughput Full Genome Sequencing of 2009 Swine H1N1 Isolates From World Wide Origins
Huo-Shu Houng, Ph.D., Viral Disease, Walter Reed Army Institute of Research
Novel 2009 inluenza A (H1N1) is a new flu virus of swine origin that was first detected in Mexico and the United States in March/April 2009. We systematically investigate the potential of ultra-deep pyrosequencing to determine and assemble full genome sequences of H1N1 viruses from world-wide geographic origins. A robust RT-PCR protocol was established to efficiently amplify across the boards of all 8 2009 novel H1N1 RNAs into sufficient cDNA quantities using the Roche 454 FLX system.
9:50 ChIP DNA Sequencing on Second Generation Technologies and Applications in Genomic Researches
Huihuang Yan, Ph.D., Great Lakes Bioenergy Research Center, University of Wisconsin
The US DOE Joint Genome Institute (JGI) is a high-throughput sequencing and genomic research center involved in a myriad of sequencing projects. JGI’s major effort is the sequencing of genomes and transcriptomes of plants, fungi, microbes and environmental metagenomic samples of relevance to the DOE missions of carbon sequestration, bioremediation and energy production. We at JGI developed molecular approach to unbiasedly amplify ChIP DNA and applied the amplified products to these two sequencing platforms. We utilized this approach to study microbial transcription start sites, centromere structure in plant and transcriptional coactivator binding site in mouse. I am going to present laboratory procedures, data analysis strategies and results.
10:20 Technology Spotlight Sponsored by 
DNA Library Preparation: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition
Nicholas Caruccio, Ph.D., Director of Market Development, EPICENTRE Biotechnologies
DNA library preparation is a common entry point for next-generation sequencing. EPICENTRE’s patented Nextera™ technology is a novel, single-tube method for preparing fragmented and tagged DNA libraries, in less than 8 hours. This flexible, scalable, and efficient technique can generate libraries for multiple next-generation sequencing platforms, whole-genome amplification, and other applications.
10:35 Networking Coffee Break, Exhibit and Poster Viewing
11:15 Applying Next-Generation Sequencing to Cancer and Medical Genetics
Stacey Gabriel, Ph.D., Co-Director, Genome Sequencing and Analysis, Broad Institute
11:45 Genome Complexity Reduction and Next-Generation DNA Sequencing in a Clinical Diagnostics Environment
Matthew Ferber, Ph.D., Co-Director of the Clinical Molecular Genetics Laboratory and Assistant Professor, Lab Medicine and Pathology, Mayo Clinic
12:15 Close of Session
Sponsored by
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12:30pm Luncheon Presentation
SOLID 3 system - It's Not Just Sequencing
Michael D. Rhodes, Ph.D., Senior Manager SOLiD Sequencing Portfolio, Applied Biosystems
Results from analysis of whole transcriptomic experiments will be presented, discussing the number of individual reads required to detect rarer transcripts. The ability to detect gene fusions and alternate splice variants will be discussed with particular reference to the software that enables 50 base reads to detect these structures. The results of measuring multiple small RNA samples at once and the needed coverage will be presented.
2:00 Chairperson’s Remarks
Patrice Milos, Ph.D., VP & CSO, Helicos Biosciences
2:05 Observations of the Most Abundant and Active Genes in the Biosphere—The Ecology of Viral Genes
K. Eric Wommack, Ph.D., Associate Professor, University of Delaware, Delaware Biotechnology Institute
Shawn Polson, Ph.D., Postdoctoral Fellow, University of Delaware, Delaware Biotechnology Institute
Two decades of aquatic viral ecology research have established that marine microbial communities support large viral populations with rapid turnover rates. As a consequence we can assume that most genes within aquatic viral metagenomes are actively replicated and expressed within aquatic microbial communities. Thus, one challenge for the coming third decade of the ‘third age of phage’ is to leverage metagenomic resources for an increasingly sophisticated view of the role of viral processes within microbial communities. High-throughput sequencing of viral genomic nucleic acids from environmental samples is adding exquisite genetic detail to our view of natural viral assemblages. It is quite possible that dsDNA viruses alone are among the greatest reservoirs of genetic diversity in the biosphere. Our recent work indicates that even the most commonly encountered genes within viral assemblages are largely unknown, showing no homology to previously sequenced genes. This talk will review the current status of viral metagenomics and propose paths forward to meeting the challenge of understanding the ecological significance of abundant and active viral genes.
2:45 Transcriptome-Guided Characterization of Genomic Alterations
Qi Zhao, Ph.D., Assistant Professor, Human Genomics Medicine, J. Craig Venter Institute
We have identified new genomic alterations in a breast cancer cell line using high-throughput transcriptome sequencing. With cDNA sequences captured by 454 reads, we were able to identify genomic rearrangement events leading to fusions or truncations of genes already implicated in oncogenesis and other additional genes . Our approach demonstrates that high-throughput transcriptome sequencing is an effective strategy for the characterization of genomic changes in cancers.
3:15 Networking Refreshment Break and Final Exhibit and Poster Viewing
3:45 Detecting Signatures of Domestication in the Chicken Genome
Michael Zody, M.Sc., Chief Technologist, Broad Institute and Department of Medical Biochemistry and Microbiology, Uppsala University
We used SOLiD sequencing to generate whole genome shotgun sequence data from pools representing several different domestic chicken lines and a pool of red junglefowl. This sequencing yielded over 5 million high confidence SNPs (>99% validation rate) and more than 2,000 high confidence deletions. Analysis of variation within domestic lines showed a large number of regions of extended homozygosity within one or more domestic lines, indicating sites of likely selective sweeps during domestication or later specialization of domesticated lines.
4:15 The Vertebrate Microbiome in Health and Disease
Rob Knight, Ph.D., Assistant Professor, Department of Chemistry and Biochemistry, University of Colorado at Boulder
Frederic Bushman, Ph.D., Professor, Microbiology, University of Pennsylvania
Alterations in vertebrate-associated microbial communities have been implicated in maintaining health and alterations can accompany disease. Examples from recent studies will be presented that emphasize the dynamics and diversity of the vertebrate microbiome, and the value of Next-Generation Sequencing as an analytical tool.
5:00 Close of Meeting
Co-located Event: Next-Generation Sequencing Data Analysis
For more information, please contact:
Mary Ann Brown
Executive Director, Conferences
Cambridge Healthtech Institute
Email: mabrown@healthtech.com
Phone: 781-972-5497
For exhibit and sponsorship information, please contact:
Angela Parsons
VP, Business Development
Cambridge Healthtech Institute
Email: aparsons@healthtech.com
Phone: 781-972-5467