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Day 2

Wednesday, April 23

7:30-8:15am Conference Registration and Morning Coffee
TECH EXPO
Explore available next-generation screening platforms as presented by sequencing leaders. An unparalleled opportunity to compare and contrast these next-generation sequencing platforms to best suit your research needs.

8:15 Chairperson’s Opening Remarks

Sponsored Seminars hosted by:

8:30 True Single Molecule Sequencing: Current Research and Our Path to the $1000 Genome

Patrice M. Milos, Ph.D., Vice President and Chief Scientific Officer, Helicos
Helicos has developed a novel genetic analysis platform to efficiently and accurately determine the direct sequence of individual DNA molecules. Simplicity in sample preparation, development of novel surfaces, chemistry to enable incorporation of single nucleotides into DNA strands and finally the visualization of fluorophore addition to monitor real-time sequencing by synthesis has been achieved. This platform will provide the opportunity for researchers to interrogate the genome on a new scale and provides a path to sequence individual genomes at a cost to make integration of genome knowledge and healthcare possible. To demonstrate the current power of the HelicosTM platform we will discuss the use of the True Single Molecule Sequencing Technology (tSMSTM) for candidate gene resequencing, RNA measurements and miRNA analyses.
9:15 Illuminating the Genome 

Abizar Lakdawalla, Ph.D., Senior Product Manager, Sequencing Applications, Illumina
The Illumina Genome Analyzer, based on the Solexa massively parallel sequencing-by-synthesis technology, is being used for a broad set of functional genomics applications including chromosomal re-arrangements, to single nucleotide variations, variation in DNA methylation, whole transcriptome analysis, small RNA analysis, digital gene expression, DNA-protein, and DNA-RNA interaction analysis. Details on the current state of the technology as well as a summary of chromosomal resequencing studies, whole genome epigenetic changes, tissue-specific mRNA splice variatns and 5’-UTRs, microRNAs and DNA-protein interactions studies will be presented.

10:00 Making High Throughput Whole Genome Sequencing Routine
Todd Arnold, Ph. D., Director of Molecular Biology, Roche 454 Life Sciences
As demonstrated by over 140 peer reviewed publications, researchers havesuccessfully used the Roche/454 Genome Sequencer FLX platform for explorationand elucidation of many genome-related questions. Recent results from viralmetagenomics, whole genome sequencing of complex organisms, and varioustranscriptome studies will be presented. The GS FLX currently provides readlengths of 250 base pairs generating 400,000 reads per 7.5 hour instrument run.Advances in the system will be presented, including data demonstrating readlengths in excess of 400 base pairs, over 1 million reads per instrument run,and improved data quality. These system advancements are achieved solelythrough reagent and software updates and do not require changes to the currentGS FLX system hardware.

10:45 Networking Coffee Break, Poster and Exhibit Viewing

11:30 Interactive Panel Discussion: The $1000 Genome Threshold
Moderator: Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
The past 30 months have witnessed remarkable advances in next-generation sequencing throughput, accuracy, and results. More than 200 instruments have now been deployed in organizations around the world, and the range of questions and applications being addressed continues to astound. Together with rapid advances in consumer genomics, we are fast approaching the Holy Grail of the $1000 human genome sequence. This panel discussion will review the most recent technical advances and scientific applications of next-generation sequencing, as well as consider the practical, medical and ethical issues surrounding personalized genomics.

12:30pm Luncheon Technology Workshop 

hosted by 

Your Sequencing Machine Just Completed its Run. Now what?
Powerful “information throughput” enabling timely upstream analysis

Ron Ranauro, President and CEO, GenomeQuest, Inc.
With next-generation sequencing machines churning out data at a rate of 200 million to 1 billion bases per run, researchers are left with the daunting task of making sense of the data. In this workshop we will discuss a breakthrough technology that delivers compute power, algorithms, data management, and results analysis to manage and mine huge volumes of data, directly to your desktop.

 

DATA ANALYSIS – WHAT DOES IT TAKE?

2:00 Chairperson’s Remarks

Kick-Off Keynote Presentation
2:10 Biomedical Analysis and Applications of Large-Scale DNA Sequence Data
Nicholas J. Schork, Ph.D., Director of Research, Scripps Genomic Medicine and Professor, Molecular and Experimental Medicine, The Scripps Research Institute
This talk will focus on the analysis and potential applications of data generated by next-generation sequencing technologies, with a focus on two main themes: the analysis of individual DNA sequences in human association studies (including cancer and host-pathogen interaction studies) and an assessment of the unique nature of the human diplome.

3:00 SolexaTools: An Open Source Sequencing Framework
Brian O’Connor, Ph.D., Post-Doctorate, Human Genetics, University of California – Los Angeles
The SolexaTools project was started to meet the computation infrastructure needs of scientists using the Solexa massively parallel sequencing platform. This open source project provides two key features for the community. First, a LIMS system for tracking sequencing runs (SolexaLIMS) and, second, a pipeline framework for organizing the analysis of data (SolexaPipeline). These tools allow scientists to automate most of the processing and report generation required by Solexa data. The software is freely available and has been written to allow for customization and community driven development. Both are important given the inherent flexibility of this new sequencing technology.

3:30 Genomics of System-Specific Model Species
Matthew Hudson, Ph.D., Assistant Professor, Crop Sciences, University of Illinois
Next-generation sequencing can be used to produce low-cost genomic resources for “system specific” eukaryotic models: plants and animals which are specifically suited to a particular scientific question. While complete genome sequencing using short reads alone is not yet feasible for higher eukaryotes, current technology can provide an aid to whole-genome sequencing for smaller genomes, and a route to gene-space sequencing of larger genomes. New and adapted sequence analysis methods are necessary to facilitate these genomics projects. Results will be presented on data analysis methods and biological insights from partial genome and transcriptome sequencing using short-read technology.

4:00 Networking Refreshment Break, Poster and Exhibit Viewing

 NEXT-NEXT GENERATION SEQUENCING

4:30 SMRT (Single Molecule Real-Time) DNA  Sequencing - a Transformative Method for  High-Throughput DNA Sequencing 
Stephen Turner, Ph.D., Chief Scientific Officer, Research and  Development, Pacific Biosciences
SMRT (Single Molecule Real-Time) DNA sequencing is a novel, high-throughput method for sequencing DNA. Though the majority of DNA sequence data collected to-date has been acquired through the use of DNA polymerase enzymes, the methods used squander the inherent power of the enzyme as a sequencing engine. Viewed as a sequencing engine, DNA polymerases can ‘read’ up to 1000 bases per second per molecule, do so over DNA lengths of 100,000 bases or more, replicate with high fidelity and consume only one molecule per base ‘sequenced.’ To harness this power, Pacific Biosciences has developed a method of eavesdropping on template-directed synthesis by DNA polymerase in real-time. We show proof-of-concept data that indicates this will be a high-throughput sequencing technology with long readlengths, limited ultimately by the processivity of the enzyme and fast cycle times dictated by the incorporation rate of the enzyme.

4:55 Base Pair Discrimination via Transmission Electron Microscope 
William Glover, President, R&D, ZS Genetics
ZS Genetics (“ZSG”) is developing a Third Generation Sequencing platform to read DNA base pairs directly with a specialized Transmission Electron Microscope. Nucleotides modified with single heavy atoms provide a signal sufficient for discrimination by a sub-angstrom-resolution TEM. dsDNA, initially in the 8 kb to 12 kb range, will be linearized on a thin-membrane substrate. Both strands will be labeled and independently resolved, providing built-in error checking. Speeds for ZSG’s Beta system at the end of 2008 will be comparable to next-generation sequencing technologies and increase thereafter via automation and customization of TEM components.

5:20 Meet the Polonator!                                                                                                             Danaher Logo 2
Kevin McCarthy, Chief Technology Officer, Danaher Motion - Dover
Danaher Motion - Dover, in collaboration with the Church Laboratory of Harvard Medical School, introduces the Polonator G.007, a revolutionary approach to second-generation sequencing. The Polonator G.007 is a completely open platform, combining a high performance instrument at a very low price point, with freely downloadable, open-source software and protocols, low-cost reagents, and inexpensive flow cells. Together, the Polonator G.007 dramatically lowers both the upfront and recurring costs of entry to second-generation sequencing, while providing a robust, modular system that delivers exceptional throughput, accuracy, and reliability. Users may choose to use the standard protocols, reagents, and software as is, but are also totally free to innovate; all aspects of the system are open and programmable, providing the flexibility to support a wide range of alternative sequencing methods. 

 

5:45 Networking Reception, Poster and Exhibit Viewing

6:45 End of Day

 

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