TUESDAY, SEPTEMBER 22, 2009
7:30am Breakfast Presentation (Sponsorship opportunity available)
8:15-9:15 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 sequencing ideas, experiences, and develop future collaborations around a focused topic.
Table 1: Sequencing Applications for the Illumina Genome Analyzer II
Host: Iwanka Kozarewa, Ph.D., Sequencing Technology Development, Wellcome Trust Sanger Institute
This discussion will be focused on recently developed applications of the Illumina NGS sequencing and on troubleshooting protocols for these applications. Discussion topics include:
• Amplification-free sequencing
• Multiplexing
• Targeted sequencing
• Metagenomics
• High-throughput insertion sites sequencing
Table 2: SNP Discovery, Analysis and Confirmation Using Next-Gen Sequence Data
Hosts: Tom Schwei, General Manager, DNASTAR and Schuyler Baldwin, Senior Software Engineer, DNASTAR
• Tools for sorting through large volumes of data
• Determining significance – what information is needed?
• False positives vs. false negatives – what is my preference?
Table 3: Considerations for Experimental Design of Targeted Resequencing Studies
Host: Jeremy Lambert, Product Manager, Raindance Technologies
Discussion to include:
• Understanding coverage models and sequencing requirements
• Resequencing of Pooled Genomic DNA Samples for Population Genetics Studies
• Data standards
• Clinical resequencing
• Impact of third generation sequencing platforms
Table 4: mRNA-seq - Can We Really Still Call It "Gene Expression"?
Host: Mike Levivelt, Ph.D., VP, Genomics, Partek, Inc.
• Does alignment impact mRNA-seq?
• Are we measuring genes or transcripts?
• What do you do with the stuff that doesn't align?
Table 5: High-throughput Sequencing for Microbiome Studies
Host: Rob Knight, Ph.D., Assistant Professor, Chemistry/Biochemistry, University of Colorado at Boulder
• Read length vs. depth of coverage: What's enough for what types of study?
• Which techniques are appropriatefor clustering community data?
Table 6: Understanding and Working in Color Space
Host: Michael Zody, M.SC., Chief Technologist, Broad Institute; Uppsala University
Discussion will be focused on:
• How 2-base encoding works
• Advantages and disadvantages
• Aligning, data correction and converting to base space
Table 7: Sequencing Library Preparation: Garbage In, Garbage Out?
Host: Nicholas Caruccio, Ph.D., Director of Marketing Development, EPICENTRE Biotechnologies
Discussion will be focused on:
• Quality and quantity of starting material
• Library recovery and quantitation
• Assessment of library quantities
Table 8: Sequence Data Management and The Cloud: The Road to Discovery
Host: Ron Ranauro, CEO, GenomeQuest, Inc.
Bioinformatics managers need to move sequence data between a number of third party and open source tools. Discussion points include:
• What is the best strategy for accomplishing these goals?
• How does this strategy change if the IT resources are buried in the cloud?
• What are the IT challenges of sharing sequence data across an organization?
• What is the strategic value of a sequence data management platform approach?
Table 9: Why Not Use NGS More Frequently?
Host: Heather Koshinsky, Ph.D., Co-founder & CSO, Eureka Genomics
Discussion will be focused on:
• Acquisition costs (hardware, reagents, training)
• Quality of data & available bioinformatics software
• Characteristics of the ideal NGS service provider
• Availability of sequence generation and/or bioinformatics service providers
Table 10: NGS Five Years Down The Road
Host: Hendrik Heus, Ph.D., Scientist, GenomeQuest, Inc.
In five years time NGS will have gone from "sexy new technology" to "established and mainstream". The price of sequencing and analysis will come down, the complexity and volume will go up. What will remain from our efforts today, and what will NGS analysis look like?
KEYNOTE PRESENTATION
9:30 Chairperson’s Remarks
Robert Cook-Deegan, M.D., Director, Institute from Genome Sciences & Policy, Duke University
 9:40 John Quackenbush, Ph.D., Professor, Computational Biology & Bioinformatics, Harvard Medical School
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10:30 Networking Coffee Break, Exhibit and Poster Viewing
11:15 Beyond Data Generation: Challenges Inherent in Designing and Analyzing Experiments Using Next-Generation Sequencing
Ghia Euskirchen, Ph.D., Director of DNA Sequencing Program, Center for Genomics & Personalized Medicine, Stanford University School of Medicine
The ever-expanding availability of sequenced genomes and advances in affordable, next-generation sequencing technologies allow a myriad of ‘dream’ experiments to become attainable. For example, parallel studies to map transcription factor binding regions (ChIP-Seq), epigenetic modifications, DNase I hypersensitivity sites, transcriptomes (RNA-Seq) and polymorphisms promise to deepen our understanding of the basic principles of gene regulation. However, identifying these novel features and discerning their relationships involves a large degree of integration across protocols, platforms and datasets and remains a central challenge in the exploration of genomes. Additionally we find that reference samples are necessary to adequately score many of these datasets, and understanding the underlying characteristics of these controls has a direct effect on both the experimental design and the ensuing bioinformatics. Examples will be presented from a number of these studies as well as practical experience gained from generating, analyzing and managing next-generation sequencing data.
11:45 Epigenomic Analysis Using Massively-Parallel Sequencing
Masako Suzuki, D.V.M., Ph.D., Associate, Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine
The Einstein Center for Epigenomics is focused on testing how epigenetic dysregulation contributes to the pathogenesis of human disease. To accomplish this, Center investigators have been developing new assays based on massively-parallel sequencing, each requiring its own analytical approach. We present our experience with the management and analysis of epigenomic data in our Center.
12:15pm Close of Session
12:30 Luncheon Presentation Sponsored by .jpg?n=8509 "Corporate Technologies")
An Active Archive for Life Science Research
Dane Stout, Market Segment Manager, Life Science & Healthcare Providers, Sun Microsystems, Inc.
The Sun Active Archive for Life Sciences enables long term stewardship of Pbytes of raw and processed data, enables rapid metadata searching, and establishes relationships between data for semantic search and analysis. It builds upon proven hardware and software technology, and supports the explosive growth in Life Sciences data with a flexible, cost-effective, open environment. The Sun Active Archive for Life Sciences enables secure data preservation, retrieval, transformation and sharing of raw data, processed results, and complex relationships between them. It enables researchers to leverage vast amounts of multi-source data, continuously improve results with newer algorithms, access relevant details for broader studies, support distributed and collaborative research, and address regulatory requirements.
As never before, the sequencing data deluge has partnered platform manufactures and software developers with NGS end-users. Users quickly realize that the ease of the platform run leads to a sobering realization “Now What the Heck Do I Do with the Data?” Join software developers and NGS users in a unique session that partners the user’s data deluge with a company’s software solution leading to comprehendible biological results.
1:55 Chairperson’s Remarks
Jae Lee, Ph.D., Associate Professor, University of Virginia School of Medicine
Hosted by
2:00 Software Solution Co-Presentation
Sample Preparation to Data Analysis – Next Generation sequencing Experiences at Ambry Genetics
Tom Schwei, General Manager, DNAStar
Wei Guo, Ph.D., Bioinformatics Scientist, Ambry Genetics
Next-gen sequencing (NGS) has significantly changed the way sequencing projects are designed. Continuous improvements in accuracy and read length are bringing NGS closer to utilization in diagnostics. Ambry Genetics is providing full service solutions from sample prep to data analysis for academic and industrial clients. Applications run in our laboratory include ChIP-seq, exome or targeted resequencing with sequence capture, de novo and RNA sequencing. DNAstar software can be used to annotate amino acid changing- and splice junction variations to create easy-to-read reports for clients that do not have computational or bioinformatics support. Sample projects will be discussed showcasing DNAstar applications.
2:30 Software Solution Co-Presentation Hosted by
Transcriptome-Wide Profiling for Normal Breast Tissues
Michael Lelivelt Ph.D., Vice President of Genomics, Partek Inc.
Yunlong Liu, Assistant Professor, Medicine, Indiana University
The breast is one of the most complex genetic organs within the body. This is because the expression levels of its genes are under the control and influence of the hormonal milieu present in the circulating plasma, which changes as a function of age; and for premenopausal women as a function of the menstrual cycle. The goal of this project is to characterize molecular variability of breast tissues from volunteer donors with no clinical evidence of breast malignancy. Normal breast tissues were procured from the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center. In order to eliminate bias from stromal tissue, normal samples were laser capture microdissected for ductal cells and RNA extracted from the excised tissue. Libraries were prepared for the Applied Biosystems (ABI) SOLiD3 sequencer using the Whole Transcriptome Analysis Kit from ABI. Herein we present a preliminary analysis of the transcriptomes of normal breast tissues from two individuals. A multitude of analysis is ongoing, including but not limited to differentially expressed genes, identification of novel transcripts, and alternative splicing.
Hosted by
3:00 Software Solution Co-Presentation
Integrating Genetic & Epigenetic Data Across Array, Proteomic & NGS Platforms
Peter Grant, CEO, Genomatix Software, Inc
Adrian Platts, Bioinformatics and Computational Genetics, Center for Molecular Medicine and Genetics, Wayne State University Medical School
The male germ cell presents a remarkably rich landscape of genetic and epigenetic information. This is one of the few cells in which virtually all the RNA can be regarded as an epigenetic component. Transcript analyses (Affymetrix, Illumina) of sperm RNAs are complicated by testis-specific splicing and differential RNA degradation. Equally, the multimodal packaging as determined by Agilent aCGH and GAII-SE DNA sequencing of DNA along with ChIP-seq (GAII) of acetylation and methylation in sperm presents analytical challenges. Integrating diverse data resources at a whole genome level poses a combinatorial challenge. A solution to this complexity is afforded in the rapid automation of workflows through an end-to-end sequence analysis pipeline. These were written to integrate several open source and platform-specific tools with the core set of Genomatix sequence mapping, mining and characterization applications, contributing together to form a rich database of genomic annotations.
3:30 Networking Refreshment Break, Exhibit and Poster Viewing
4:00 Software Solution Co-Presentation Sponsored by
From ChIP-seq to Pathways. ExPlain™ Helps to Reverse-Engineer Chromatin-IP and Microarray Data on p53 Response to Anticancer Drugs
Alexander Kel, Ph.D., Senior Vice President Research and Development, BIOBASE GmbH
Martin Enge, Ph.D., MTC, Karolinska Institute, University of Helsinki, Sweden
In this talk, we will present a case study of applying novel reverse-engineering method which uses BIOBASE databases and analysis platform ExPlain™ for discovery of mechanisms of anticancer drug response. We performed a Chromatin Immunoprecipitation experiment followed by high-throughput Illumina sequencing of paired end tags (ChIP-seq) on MCF7 cancer cell line upon treatment with small-molecule p53 reactivators Nutlin and RITA and the antitumor agent 5-Fluorouracil, immunoprecipitating p53 to sequence the crosslinked DNA. ChIP-seq was combined with microarray gene expression analysis. Our novel reverse-engineering method uses the actual statistics of differential regulation of genes to assess statistical significance and takes into account both functional and physical interactions between cooperating transcription factors, as well as the mode of the TF (activation/repression/unspecified enhancer). Our analysis suggests that repression of genes by p53 is important for the induction of the apoptotic response, and that Forkhead box genes are essential co-factors of p53. Furthermore, in agreement with earlier studies, our results suggest that the sequence of the p53 binding motif itself can affect p53 binding to promoters and, hence, regulate gene expression. We applied ExPlain™ platform for upstream topological modelling of signal transduction network of these cells, which reveals causality pathways responsible for triggering activity of found co-occurring transcription factors. This analysis helped us to identify key nodes in such pathways, that can be considered as prospective anti-tumor drug targets for combinatorial cancer therapy.
4:30 Software Solution Co-Presentation (Opportunity Available)
5:00 Close of Day
Co-located Event: Exploring Next-Generation Sequencing
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