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Thursday, April 24
7:30am Breakfast Technology WorkshopA New Paradigm: Next Generation Sequencing Applications and ServicesJanet Hager, Ph.D., Product Manager, Sequencing Services, Cogenics, The Genomics Services CompanyTMAs an early implementer of Roche 454 pyrosequencing technology, Cogenics has significant experience tailoring solutions across multiple applications for de novo sequencing and resequencing. By providing dedicated study direction and seamless upstream and downstream services, study quality and data delivery are optimized in an efficient, timely and cost effective manner.
TRIALS AND TRIBULATIONS OF SETTING UP A NEXT-GENERATION SEQUENCING LAB
8:30 Chairperson’s Remarks
8:35 Baylor College of Medicine: Donna M. Muzny, M.Sc., Director of Operations, Human Genome Sequencing CenterProduction Sequencing in the Next-Generation Environment: Next-Generation sequencing platforms and chemistry such as 454, Solexa and Solid instrumentation has ushered in a new era in sequencing technology, allowing for new and innovative experimental strategies involving sequencing, where before, due to time and cost were prohibitive. The BCM-HGSC is in a unique position to evaluate all three sequencing chemistries and platforms, however much work is still required to optimize these sequencing instruments and pipelines for mainstream production. Understanding basic techniques involved, the limitations and processing parameters has enabled optimization of the pipelines and greater opportunity for applications. Our current challenge is the production ramp of the 454 sequence pipeline for the maximum utility of ten 454 FLX instruments.
9:00 Broad Institute: Andrew J. Barry, Supervisor, Process Development, Genomic Sequencing, Broad Institute
Evaluation, Validation, Development and Scale-up of Next-Generation Sequencing Platforms at the Broad Institute of MIT and Harvard: Currently, the Broad Institute’s Technology Development Group has four next-generation sequencing platforms in various stages of the transition from evaluation to robust production scale processes. Each step in this progression has specific validation specifications that must be met in order for the technology to advance. Initial evaluation and validation follows a very similar sequence across technologies, with a predetermined set of validation samples processed across platforms. Once this is accomplished, a decision is made as to whether the technology will or will not be developed into a large-scale production process. My talk will focus on the development and scale-up of next-generation sequencing platforms into robust and efficient production processes.
9:25 DOE Joint Genome Institute: Daniel Rokhsar, Ph.D., Program Head, Computational Genomics
9:50 Networking Coffee Break, Poster and Exhibit Viewing
10:30 J.Craig Venter Institute: Robert Strausberg, Ph.D., Deputy DirectorEmerging DNA Sequencing Technologies: New Platforms for Human Genomic Medicine: Recently we described the diploid genome sequence of an individual human [Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) PLoS Biol 5(10): e254.] Current progress with advanced technologies suggests that the sequencing of thousands of individual human genomes will be achievable over the next decade. This presentation will focus on the challenges and opportunities presented by next-generation sequencing technologies to enable new applications in human genomic medicine.
10:55 Washington University: Vincent Magrini, Ph.D., Senior Scientist, Genetics Sequencing CenterNext Gen: From Beta to Production? Achieving low-cost and high volume DNA sequencing data generates a dynamic next-generation platform environment. The radical changes/modification from Sanger-based sequencing and associated instrumentation warrants early access investigation and evaluation which focuses on molecular manipulations, instrument robustness /data quality, and infrastructure support as to handle large data sets. Early access investigation is also associated with platform-specific growing pains and requires trouble shooting instrumentation hardware/software failures and poor/incomplete chemistries with the ultimate goal of minimizing instrument downtime and establishing production-ready high throughput DNA sequencers.
11:20 Interactive Panel Discussion with Morning SpeakersModerator: Kevin Davies, Ph.D., Editor-in-Chief, BioIT WorldThe rise of several commercial next-generation sequencing platforms in the past two years has in many ways democratized the science of genomics. No longer are high-throughput genome analysis projects confined to genome sequencing centers. But what key issues must be addressed to make the investment work? How can organizations lacking robust IT support manage the torrents of data produced? What are the best approaches for data management and analysis? We will discuss these questions and more with experts who have confronted, and possibly overcome, these challenges.
EXPANDING THE ENVELOPE OF APPLICATIONS
1:30 Chairperson’s Remarks 1:35 Sequencing more Human Genomes by the Next-Generation TechnologyJun Wang, Ph.D., Professor, Associate Director, Beijing Genomics InstituteNew 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.
2:05 Sequencing-Based Survey of Transcriptional Complexity and Regulation Masayoshi Itoh, Ph.D., Senior Scientist, LSA Technology Development Group, Omics Science Center, RIKENThe genome sequence is an invaluable resource, but it is only the initial step towards the functional categorization of the genes, RNAs and other functional genome elements. Despite there are less than 25,000 protein coding genes, mammalian genomes express at least 181,000 different RNAs, which constitute more than 44,000 transcriptional units (TUs). Up to 93% of the genome is transcribed as primary RNA. The development of novel generation of sequencing instruments allows addressing the RNA complexity at a much higher definition. We are using the 454 Life Science, Illumina/Solexa and ABI-SOLiD sequencers to produce hundreds of millions of sequences tags, including the CAGE (cap-analysis gene expression) and short RNA libraries. Sequencing-Based transcriptome analysis produces much more detailed and sensitive data than microarrays, at a similar cost. CAGE analysis identifies and maps more than 230,000 core promoters, resulting in a finely redefinition of the promoter structure. CAGE analysis allows correlating promoter elements to transcription, paving the way to decipher detailed transcriptional networks in mammalians. In the next few years, deep sequencing of functional libraries derived from various RNA classes will allow a broad, quantitative and systematic approach to biological problems.
2:35 Deep Transcriptome Sequencing in Schizophrenia Stephen Kingsmore, Ph.D., President, National Center for Genome Resources
We ascertained the genetic architecture of schizophrenia, a common, severe psychiatric illness with high heritability, by Solexa/Illumina sequencing of polyadenylated RNA from cerebellar cortices of eleven unrelated cases. One gigabase of clonal, sequencing-by-synthesis reads afford coverage of most transcripts sufficient for identification of known and novel coding nucleotide variants, alternative splicing and digital expression, enabling detection of allelic effects on transcript and isoform expression. Among 18,974 genes expressed in cerebellum, 142 exhibited non-synonymous or functional variants in most or all patients. Of these, seven were established candidate genes. An additional 95 established candidate genes contained non-synonymous or functional variants in a minority of patients, quantitatively substantiating locus and allelic heterogeneity of schizophrenia.
3:05 Sequencing Needs in Newborn ScreeningPatricia W. Mueller, Ph.D., Chief, Molecular Risk Assessment Laboratory, Newborn Screening and Molecular Biology Branch, Centers for Disease Control and Prevention (CDC)
Every infant in the United States is screened shortly after birth using heel stick blood spots to detect a variety of congenital conditions using chemical and biochemical tests. A variety of genes and many mutations within those genes contribute to most of these diseases. Increasingly, there is a need to identify the specific mutations for confirmation and because of new treatment options for specific types of mutations. The spectrum of mutations is complex, including single nucleotide polymorphisms (SNPs), premature stop codons, small insertions and deletions, whole gene deletions, and pseudogene chimeras. This important public health need will benefit from application of the sequencing and copy number variant (CNV) technologies currently under development.
3:35 Networking Refreshment Break, Last Chance for Poster and Exhibit Viewing 4:00 Digital Allelotyping Revealed Tissue-Specific and Allele-Specific Gene Expression in the Human GenomeKun Zhang, Ph.D., Assistant Professor, Department of Bioengineering, University of California, San DiegoWe developed a digital allelotyping method by capturing exonic SNPs with padlock probes and single molecule sequencing. We applied this method to three cell lines established from different tissues of a human subject in the Personal Genome Project. We identified a large number of genes that showed tissue-specific and allele-specific gene expression, suggesting the presence of tissue-specific cis-regulatory polymorphisms. Our study highlighted the complicated landscape of tissue-specific cis-regulation in the human genome.
4:30 Characterization of the Vertebrate Regeneration Epigenome and a Genomic Survey of the Axolotl Salamander (Ambystoma mexicanum)Gerald Pao, Ph.D., Research Associate, Laboratory of Genetics, The Salk Institute for Biological StudiesThe axolotl (Ambystoma mexicanum) is a diploid salamander capable of remarkable regenerative capacity upon injury. Prior to our work virtually no genomic sequence was known of this organism, although it was known that the axolotl genome is roughly 10 fold larger than the human genome (approx. 3.2 X 1010 bases) with 14 chromosome pairs. In the present project we have used a combination of Chromatin Immunprecipitation, shotgun genomic, cDNA, small RNA and limited Bacterial artificial chromosome clone using massively parallel 454 sequencing to formulate testable hypotheses on the nature of the regenerative process and simultaneously characterizing an extraordinarily large genome. The results demonstrate the utility of this technology for the characterization of unsequenced large genomes with low complexity. Results thus far from several rounds of ChIP sequencing have revealed a number of candidate genomic regions activated during regeneration. In addition we have validated our experimental approach of ChIP sequencing for genomes without a prior reference genome with 454 massively parallel sequencing technology. In addition to ChIP sequencing of transcriptionally active regions we have had deep sequencing runs of the small RNA component, the transcriptome as cDNAs and a small number of BACs. Preliminary results show the upregulation of mRNAs and small RNAs consistent with the induction of a stem cell state in the early steps of regeneration. Furthermore, shotgun sequencing of the genome reveals an interesting repetitive element content that markedly differs from the mouse and human genomes.
5:00 Highly Integrated Single Base Resolution Maps of the Epigenome in ArabidopsisRyan Lister, Ph.D., Plant Biology Laboratory, The Salk Institute for Biological StudiesBy regulating transcriptional potential of the genome, the epigenome plays a pivotal role in cellular differentiation, organogenesis, tissue formation, and aging. Deciphering the multiple layers of epigenetic regulation that control transcription is critical to understanding how plants develop and respond to their environment. Using sequencing-by-synthesis technology we directly sequenced the cytosine methylome, transcriptome, and small RNA transcriptome to generate highly integrated epigenome maps for wild-type Arabidopsis thaliana and mutants defective in DNA methyltransferase or demethylase activity. At single-base resolution we discovered extensive, previously undetected, DNA methylation, identified the context and level of methylation at each site, and observed local sequence effects upon methylation state. Deep sequencing of smRNAs revealed a direct relationship between the location of smRNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylation, and a tendency for smRNAs to direct strand-specific DNA methylation in regions of RNA-DNA homology. Finally, strand-specific mRNA-seq revealed altered transcript abundance of hundreds of genes, transposons and unannotated intergenic transcripts upon modification of the DNA methylation state.
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