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Next-Generation Sequencing Data Analysis - Day 1



Pre-Conference Short Course
2:00-5:00pm – Separate Registration Required 


Short Course Instructors:

Chris Dagdigian, Founding Partner and Director of Technology, BioTeam, Inc.

Jacob Farmer, Chief Technology Officer, Cambridge Computer
Matthew Trunnell, Manager, Research Computing, Broad Institute 

For full programming, please click here 



7:00 am Conference Registration and Morning Coffee 



8:15 Chairperson’s Remarks
Kevin Davies, Ph.D., Editor-in-Chief, BioIT World

John Rothberg8:25 Moore’s Law and Sequencing: Where Are We Now, Where Will it Lead, and How Will We Get There?

Jonathan Rothberg, Ph.D., Chief Executive Officer & Founder, Ion Torrent Systems, Inc.





Henry Erlich9:05 Diagnostic Applications of Next-Generation Sequencing: High-Throughput, High Resolution HLA Typing

Henry Erlich, Ph.D., Vice President, Discovery Research, Roche Molecular Systems





9:45 Networking Coffee Break

Robert Cook-Deegan10:15 So My Genome Costs Less Than My Bike: What’s the Big Deal?

Robert Cook-Deegan, M.D., Director, Institute for Genome Sciences & Policy, Duke University





Stephan Dietrich10:55 The Future of NGS from a Medical Practice Perspective

Dietrich Stephan, Ph.D., Co-founder & Chief Science Officer, Navigenics, Inc.





11:35       Interactive Panel Discussion with Keynote Speakers

12:00pm  Close of Session


12:15       Luncheon Presentation Sponsored by

NextGen Sequence Analysis Using HPC in the Clouds 
Jason Stowe, Founder and CEO, Cycle Computing
The game is changing as scientists have inexpensive access to larger amounts of genome data.   At the same time, large numbers of servers can be provisioned quickly and inexpensively in the cloud offering potential solutions for sequence analysis. For researchers that rely on high performance computation to analyze these growing data sets, the promise of utility computing will change the way science gets done. Access to hundreds or thousands of CPUs is potentially very powerful, but it leads to the question: "How do I use them to get work done?"
CycleCloud makes this easy by creating secured, managed, HPC clusters in the cloud that auto-scale to the workloads you place on them. This session will focus on:
- HPC use cases for life sciences including BLAST, sequence analysis and assembly
- Challenges and strategies for dealing with data and computation in the cloud
- Time to scientific result and cost saving using cloud resources
- Security considerations in using cloud resources.


Next-Generation Sequencing is alive, thriving, and driving discovery. As costs come down and ease increases, these new, massively parallel high-throughput sequencing platforms are infiltrating multiple aspects of traditional biological research. However, each next-generation sequencing platform best lends itself to specific sequencing goals. This Tech Expo showcases the next-generation sequencing platforms to help you make informed purchasing decisions. 

2:00 pm   Chairperson’s Remarks

Kevin Davies, Ph.D., Editor-in-Chief, BioIT World

Roche 454
Sponsored Seminars hosted by:

2:05        Roche/454
Sequencing the Whole Human Exome with the 454 GS FLX: From Mendelian Disease to Cancer Studies
Timothy Harkins, Ph.D., Genome Sequencing, Roche Applied Science, Roche, Inc.
By using Titanium Sequence Capture technologies developed by Roche NimbleGen, it is now possible to readily sequence over 170,000 exons within the human genome.  We will present a series of projects that define the performance of combining the sequence capture arrays with the Genome Sequencer FLX.  These projects include the analysis of publicly available reference genomes to assess what coverage models are needed to indentify genetic variants within the human exome.  Additional projects will be presented that demonstrate the practice of using these two technologies to indentify novel mutations that arise in cancer and also the effectiveness of indentifying mutations in Mendelian diseases.

Applied Bio2:35        Applied Biosystems
SOLiD™ 3 System - A Revolutionary Sequencing System

Michael D. Rhodes, Ph.D., Senior Manager SOLiD Sequencing Portfolio, Applied Biosystems
The SOLiD™ 3 System is the ultra high throughput sequencing system have recently demonstrated a run of 50 Mega bases of matched sequence on the human genome. The system uses a unique ligation based chemistry that offers many advantages over conventional polymerase based systems. Data will be presented on how the use of emulsion PCR and small 1µm beads allows deposition at extremely high density allowing high throughput to be achieved without lengthening run time. The unique properties of ligation based sequencing allow the use of error correcting algorithms driving the very high accuracy of the system, data on future improvements to this will be presented. These features allow genomic, transcriptomic and epigenetic applications to be carried out.

3:05        Illumina
Transforming Biology - The Illumina Genome Analyzer Now Generation Sequencer
Abizar Lakdawalla, Ph.D., Senior Product Manager, Sequencing Systems, Illumina
The Genome Analyzer massively parallel next generation DNA sequencer has revolutionized our understanding of molecular biology by revealing information on the genome, epigenome, transcriptome, and the protein-nucleic acid interactome that had not even been imagined before. With a unique combination of very high ease of use, greatest experimental flexibility and maximal yield of high data quality, the Genome Analyzer has facilitated the highest rate of publication. The presentation will focus on a technical description of the Genome Analyzer system, the breadth of applications available, and a discussion of the results and discoveries.  

3:35        Networking Refreshment Break 


4:00        Helicos Helicos 
Helicos Single Molecule Sequencing: Delivering Accurate, Quantitative Information for Genome Biology
Patrice M. Milos, Ph.D., Vice President and Chief Scientific Officer, Helicos BioSciences Corporation
Helicos True Single Molecule Sequencing (tSMS)TM  provides a unique view of genome biology through direct sequencing of cellular nucleic acids in an unbiased manner providing both quantitation and sequence information.  Using a simple sample preparation involving no ligation or PCR amplification genomic DNA is sheared, tailed with poly A and hybridized to the flow cell surface containing oligo dT for initiating sequencing by synthesis.  Helicos technology has been used successfully to sequence an array of bacteria representing the diverse genomic content of microorganisms, C. elegans and a human genome.  The highly accurate quantitation of the platform is demonstrated in our gene expression, ChIP and copy number variation studies. The simple nature of the sample preparation has allowed the direct sequencing of nucleic acid from a variety of sample types including formalin-fixed paraffin embedded tissue and archival tissue samples. We have also optimized our sample preparation to allow preparation and sequencing from picogram quantities of nucleic acid – all important for maximizing researchers ability to perform important biological experiments with limiting biological sample amounts.  A perspective on the importance of the Helicos TM Genetic Analysis System performance for a future of genomic biology with special emphasis on cancer biology will be highlighted.

 4:30       Dover   Dover Meet the Polonator
Kevin McCarthy, Chief Technical Officer, Danaher Precision Systems, Dover
Dover presents an introduction to the Polonator Second Generation sequencing platform, featuring the instrument, sequencing chemistry, operation, software, and output data.  Developed in collaboration with the Church Lab at Harvard Medical School, the Polonator combines a very low instrument cost with a robust hardware and software platform, and a compelling cost per tag.  The system is easy to use, with newly developed GUIs for running standard chemistry.  Due to its open source software, advanced users can easily adapt the instrument to develop alternative sequencing chemistries. 

5:00        Complete Genomics 

Applying Third-Generation Sequencing to Discovery ResearchComplete Genomics
Aaron Solomon, Vice President of Business Development, Complete Genomics, Inc
We will describe a novel highly accurate, high-throughput, inexpensive genome sequencing technology based on submicron DNA nano-ball™arrays and unchained base reading using combinatorial probe-anchor ligation (cPAL™) chemistry.  These advances reduce both reagent consumption and imaging time and enable Complete Genomics, Inc. to offer a sequencing service at its own commercial-scale genome center at large-scale cost of $5,000 per diploid human genome. We will present results from at least one complete human genome sequenced by Complete Genomics’ third-generation technology, confirming its ability to produce the industry’s first high quality human genome sequences at a medically-relevant cost and scale; and provide an example of how our service is used by a basic researcher.



5:30        Panel Discussion with Platform Providers

Moderator; Kevin Davies, Ph.D., Editor-in-Chief, BioIT World

Speakers from next-generation platform providers above will trade tips and insights on the latest scientific and technological advances, and answer your questions.

6:00        Welcoming Reception and Grand Opening of Exhibit Hall

7:30        Close of Day



Co-located Event:    Exploring Next-Generation Sequencing 

For more information, please contact:

Mary Ann Brown
Executive Director, Conferences
Cambridge Healthtech Institute
Phone: 781-972-5497

For exhibit and sponsorship information, please contact:
Angela Parsons
VP, Business Development
Cambridge Healthtech Institute
Phone: 781-972-5467

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