WEDNESDAY, MARCH 21
7:30-8:30 Registration and Morning Coffee

8:30 Chair’s Opening Remarks

8:40 Next Generation Sequencing; 454 Sequencing on the Roche Genome Sequencer
Michael Egholm, Ph.D., Vice President, Molecular Biology, 454 LifeSciences
In 2005 we launched the first Next Generation Sequencer which is rapidlybecoming the new standard for sequencing-based applications as evidencedby numerous peer reviewed articles in the most prestigious journals. Achallenge for the Next Generation Sequencing Systems has been short readlength to overcome the complexity of nearly all genomes. With thelaunch of the Genome Sequencer FLX system these barriers have beengreatly reduced with average read lengths of 250 bases. The FLX systemwill be described in detail including how highly accurate de novo readsare obtained and assembled. More importantly, several examples oftraditional and novel applications of ultra high throughput sequencingwill be presented.

9:30 The Next Generation is SOLID. Key Developments in the SOLiD™ System
Michael Rhodes, Ph.D., Applications Manager, High Throughput Discovery, Applied Biosystems
We describe here the development of a novel DNA sequencing technology. In this massively parallel approach, short fragment DNA populations are clonally amplified onto 1-micron beads, enriched and randomly deposited and attached onto glass arrays. The bead arrays are then placed into an automated flow cell where 4-color, fluorescently-labeled reagents are used to interrogate known template positions, and are delivered serially to sequence DNA strands. We demonstrate the use of DNA ligase and cleavable ligation substrates that allow bases to be recorded every 4th and 5th position of the template population. By serial stripping and sequencing the template with 5 offset sequencing primers and combining the results, all bases of the template are elucidated over a defined length. Attributes of sequential cycles of ligation and cleavage using 2-base encoded, 4-color fluorescently-labeled oligonucleotides include reduced signal-to-noise ratios and long read lengths, sequencing in both directions (5’ and 3’ sequencing) and enhanced ability for SNP detection.

10:20 Coffee, Poster and Exhibit Viewing

11:00 Roundtable Discussion
The $1000 Genome: Are We There Yet?
Host: Kevin Davies, Ph.D., Editor-in-Chief, BioIT World
Over the past few years, exciting advances in next-generation sequencing technology have seen the production of commercial instruments capable of profound improvements in sequence throughput and economy. Early applications include cancer genome analysis, microbial genomics, and the study of the Neanderthal genome. Competition in the field is increasingly intense, with start-ups vying with established life science instrument makers to provide the gold-standard technology that will drive us towards the threshold of the "$1000 genome.”
The expert panelists in this roundtable will review the current state of next-generation sequencing technologies and look ahead to new applications in science and medicine as well as highlight the many challenges that lay in store.

Panelists:
Michael Egholm, Ph.D., Vice President, Molecular Biology, 454 Life
Sciences
Michael Rhodes, Ph.D., Applications Manager, High Throughput Discovery, Applied Biosystems
Eddy Rubin, M.D., Ph.D., Director, Joint Genome Institute, Lawrence Berkeley National Laboratories
Jay Shendure, Ph.D., Department of Genetics, Harvard Medical School
Robert L. Strausberg, Ph.D., President, The Center for Advancement of Genomics, The J. Craig Venter Institute

12:00 Lunch on Own or Technology Workshop (Sponsorships Available)

NEXT GENERATION SEQUENCING - APPLICATIONS

1:30 Chair’s Remarks

2:20 Expanding the Search for Cancer Mutations with Advanced Sequencing Technologies
Robert L. Strausberg, Ph.D., President, The Center for Advancement of Genomics, The J. Craig Venter Institute 
The development and application of high-throughput DNA sequencing approaches for identfication of somatic mutations in cancer will be discussed. The presentation will highlight examples of the complementary utilities of Sanger and pyrosequencing technologies in the detection of mutations in glioblastoma and other cancers.

3:15 Refreshment Break, Poster and Exhibit Viewing

4:00 Seeing Variation in Genomes: 
Novel Means for Sequencing DNA
Kalim Mir, Ph.D., Wellcome Trust Fellow, Principal Investigator, The Wellcome Trust Centre for Human Genetics, University of Oxford 
We are interested in developing new technologies for sequencing specific regions of the genome in a large number of individuals and in obtaining sequence reads in a long range context. I will provide experimental details of a novel sequencing biochemistry named Cyclic Ligation and Cleavage (CLiC) that we have developed and will describe strategies for targeted “medical” sequencing. I will also introduce a novel platform for sorting, elongating and viewing long single genomic DNA molecules on a microarray and will describe a strategy for obtaining sequence reads directly upon each molecule.

4:35 From QTLs to Biomarkers for Neuropsychiatric Illnesses
Mark Brennan, Ph.D., CSO, SureGene LLC
SureGene's LocusLock™ technology takes as a starting point a whole-autosome scan for QTLs affecting various aspects of psychopathology in the normal population. Next, it couples proprietary bioinformatics strategies with linkage and association approaches in patient populations to define risk-associated haplotypes in novel candidate genes that can be resequenced to define important genetic variants. LocusLock™ focuses on the genes with the largest contributions to phenotypic variation -- arguably those of highest clinical relevance. The talk will provide examples of how specificity of phenotype, quantitative genetics, and novel bioinformatics strategies can facilitate biomarker development for complex genetic diseases.

5:10 Panel Discussion

5:45 Networking Reception

7:00 Close of Day