MONDAY, SEPTEMBER 22
7:30 am Registration and Morning Coffee
Data Generation: Sequencing Centers “Navigating the Expressway”
8:30 Chairperson’s Opening Remarks
W. Richard McCombie, Ph.D., Professor, Cold Spring Harbor Laboratory
8:45 Keynote Presentation
Next-Generation Sequencing: The Informatics Angle
Gabor Marth, D.Sc., Assistant Professor, Department of Biology, Boston College
9:30 Northwestern University
Scalable Bioinformatics for Next-Generation Sequencing
Jared Flatow, B.S.E.E., Analyst/Programmer, Bioinformatics Core
In order to keep up with the massive amounts of data produced by next-generation sequencing technologies, bioinformaticists need a way of scaling existing tools without completely redesigning them. An understanding of the industrial strength map-reduce paradigm will be invaluable to those looking to cope with the next-generation datasets. Combined with the power of elastic computing clouds, many of the potential barriers to dealing with such large-scale data can be completely eliminated. This talk will explain what map-reduce is, demonstrate how it can be used to formulate some classic bioinformatics problems and discuss how it compares to other ways of parallelizing computations, such as Message Passing Interface (MPI).
10:00 Morning Coffee
SHARED SESSION ON COMPREHENDING THE GENETICS OF HEALTH AND DISEASE
10:20 Tiling Array Analysis of DNA Copy Number Variation
Herbert Auer, M.S., Director of the Functional Genomics Core, Institute for Research in Biomedicine
New research has shown that a significant portion of the genome can vary in the number of copies of DNA elements and that this copy number variation (CNV) contributes substantially to genotypic and phenotypic variation between individuals. The presentation describes the first-time usage of tiling arrays to measure CNVs at an unprecedented 35 base pair resolution across the entire genome. Comparison of normal individuals provides information about CNVs at a resolution two orders of magnitude better than any of the currently used microarray platforms. This method can be applied to a broad range of organisms, including human, mouse, rat, arabidopsis etc., where tiling arrays are commercially available.
10:50 Common Gene Copy Number Variations in Health and Disease
Yee Ling Wu, The Research Institute at the Nationwide Children’s Hospital, Ohio State University
Results of microarray experiments reveal that many genomic loci in mammals manifest frequent copy number variations (CNVs) among different individuals. Some of these CNV loci appear to be modular or segmental and involve multiple contiguous genes, with discrete and continuous variation in copy numbers. Gene copy number variation is an important mechanism contributing to quantitative traits and phenotypic diversities. Accurate and sensitive detection of CNV is essential for genetic and mechanistic studies of complex diseases. This talk will present specific examples to elucidate complex CNVs and their associations with human autoimmune diseases.
11:20 A Musical Score for Disease
Gil Alterovitz, Ph.D., Research Fellow, Harvard Medical School
11:50 Close of Session
12:00pm Luncheon Technology Workshop Sponsored by 
Data Analysis and Interpretation: Software Solutions “Take a Test Drive”
2:00 Chairperson’s Remarks
Anton Nekrutenko, Ph.D., Associate Professor, Penn State University
2:05 Creating Bioinformatics Processes and an IT Infrastructure That Transforms Next-Generation Sequencing Data into Functional Knowledge
sponsored by 
Ron Ranauro, President & Chief Executive Officer, GenomeQuest, Inc.
Low-cost, high-throughput DNA sequencing promises to transform scientific research and usher in the era of personalized medicine. However, the current output of raw sequencing data is enormous, and requires large-scale bioinformatics processing before research can proceed. The infrastructure for this is beyond the reach of all but the most advanced staffs and largest bio-IT budgets. A Web-enabled sequencing informatics service that combines workflow consultation with large-scale data and computational resources delivers actionable scientific information quickly and at a fraction of the cost. We will discuss: the challenges to sequence informatics posed by Next-Gen data volumes; consider a sampling of build-or-buy options for your Next-Gen bioinformatics infrastructure and walk through a case example workflow customization and information delivery methods
2:35 Tools to Manage the Next-Generation Data Flood
W. Richard McCombie, Ph.D., Professor, Cold Spring Harbor Laboratory
3:05 Selected Poster Presentation
3:20 Refreshment Break
4:00 GalaxySR: A Web-Based Application for Analysis of Next-Generation Sequencing Data
Anton Nekrutenko, Ph.D., Associate Professor, Center for Comparative Genomics and Bioinformatics, Penn State University
When a researcher submits samples for next-generation sequencing, they typically receive results as a collection of very large files. At present there are no integrated sets of tools for QC, filtering, aligning, and interpreting short reads often leaving experimental biologists stuck with the data they paid a significant price to obtain. We are presenting the first freely available resource for short-read analyses that requires nothing more than a web-browser. It is built using our highly successful open-source Galaxy system. While using this system (GalaxySR) a researcher simply uploads sequences and base quality scores, surveys and filters the data, aligns reads against appropriate databases, interprets these alignments, and visualizes the results – all of this within a single portal with nothing to install or configure.
4:30 Software Drive Company I Sponsored by .jpg "DNAStar")
Insights from the Genomes of Commonly Used E. coli Lab Strains
Tim Durfee, Ph.D., Scientist, Department of Genetics, University of Wisconsin
Matthew Keyser, MS, Next Generation Applications Scientist, DNASTAR
Our laboratory has been involved in the study of microbial genetics for over 20 years. The objective of this project was to utilize Next Generation sequencing technologies to increase our depth of knowledge into strain differentiation. The collective information obtained will provide insights into the levels of genetic variation that exists within strains. Key elements of the session will include:
- Discussion of the ease of assembly complete bacterial genomes using the Roche 454 and Illumina sequencing platforms,
- Discussion of the level of synteny and polymorphism that can be seen when sequencing common bacteria, and
- Discussion that while classical genetic methods yield desired traits, many polymorphisms remain that we still not understand their relevance
5:00 Software Drive Company II Sponsored by 
Next Generation Data Analysis for Next Generation Sequencing
Nancy Bretschneider, Ph.D., Genomatix Software GmbH
The large amounts of data derived from next generation sequencing projects makes efficient data mining strategies necessary. Methods for the analysis of RNA-Seq as well as for ChIP-Seq analyzes will be presented. Based on examples we will show the possibilities for extending genome annotation, discovery of new transcriptional units and splice variant detection. In addition the down stream biological mining of enriched regions from ChIP-Seq will be demonstrated (for transcription factors and epigenetic modifications). New insights into biological mechanisms can be gained by overlaying data from different experiment types.
5:30 Grand Opening of the Exhibit Hall
7:00 Close of Day