7:30 Breakfast Technology Workshop (Sponsorship Available)

1000 DOLLAR GENOME – NEW TECHNOLOGIES

8:15 Chair’s Remarks

8:20 Single-Molecule, Motion-Based DNA Sequencing using RNA Polymerase
William Greenleaf, Graduate Student, Applied Physics, Stanford University 
We present a method for sequencing DNA using the motion of single RNA polymerase molecules. By using an ultra-stable optical trapping assay to monitor transcription when a single nucleotide species is rate-limiting, we observe distinct pauses in transcription corresponding to the DNA template positions that require this limiting nucleotide. From the aligned patterns of pauses recorded from four polymerase molecules, each observed holding a different nucleotide species rate-limiting, we determined the sequence of a section of the DNA template. This proof of principle demonstrates that the motion of a processive nucleic acid enzyme may be used to extract sequence information directly from DNA.

8:50 Nanotech Approaches and Challenges to Next Generation Sequencing and Genotyping Diagnostics
Michael J. Heller, Ph.D., Departments of Bioengineering/Electrical and Computer Engineering, University of California, San Diego
A variety of technologies have now been developed for DNA sequencing/genotyping diagnostic applications. Nevertheless, even more highly advanced technologies will be necessary to carry out the sequencing of an individual’s entire genome to determine a person’s complete predisposition to disease, drug toxicity, or drug ineffectiveness. Such novel technologies include advanced DNA nanoarrays and nanopore sequencings systems now being developed by academic, government and biotech industry researchers. Enabling these new diagnostic technologies will require that a variety of very difficult challenges be overcome, including speed, accuracy, reliability, and cost ($1000 Genome Project). We are attempting to develop unique nanoparticle discrimination mechanisms that are designed to carry out the high fidelity genotyping of the human genome in a highly reliable and cost effective manner. 

9:20 Development of the Microchip-based NanoBioPrepSEQ Station for Fluorescent DNA Sequencing Sample Preparation
Stevan B. Jovanovich, Ph.D., President, Microchip Biotechnologies, Inc.
We describe a new microfluidic and nanofluidic platform developed at MBI, the NanoBioPrepSEQ station, that integrates nanoliter-scale cycle sequencing with integrated bead-based cleanup to automate fluorescent DNA sequencing sample preparation. The NanoBioPrepSEQ combines our patented NanoBioProcessorTM technology that produces novel microscale valves, pumps, and routers on-microchips with simple control of their operation using full-scale pneumatics with full-scale commercial robotics to load and unload NanoBioProcessor microchips. The user will input standard microtiter plates with PCR products, plasmids, or other DNA templates and the robot will load the microchip that will perform nanoscale cycle sequencing and sample cleanup. The user will receive back Ready-to-Inject? microtiter plates with samples ready for long read capillary array electrophoresis analysis, saving reagent and personnel costs. We will describe the overall system and present results of the performance of this innovative platform for DNA sequencing, as well as additional applications of the technology.

9:50 Coffee Break, Poster and Exhibit Viewing

10:30 Multiplex Amplification and Sequencing of the Human Coding Sequences
Jay Shendure, Ph.D., Department of Genetics, Harvard Medical School 
We have developed a novel technology for highly multiplex DNA sequencing based on polony bead amplification and a ligation-based sequencing biochemistry (Shendure et al. 2005). To complement this technology, as well as other next-generation sequencing technologies, we have been working on methods for using oligonucleotides pools generated via programmable synthesis on DNA microarrays for multiplex targeted amplification of tens of thousands of exons in a single reaction. We hope that our approach will enable resequencing of the coding sequences of human genomes derived from normal and diseased samples in a manner that is high-throughput, efficient, and highly cost-effective.

11:00 The Archon XPRIZE for Genomics
Laurence H. Kedes, M.D., Scientific Director, Archon X PRIZE in Genomics, X PRIZE Foundation, Santa Monica, and Director, Institute For Genetic Medicine, University of Southern California
The $10 million Archon X PRIZE for Genomics is a global competition to develop breakthrough technology that dramatically reduces the time and cost of sequencing human genomes and accelerates the onset of a new era of personalized, predictive and preventive medicine. The competition guidelines and development of the rules for winning the purse will be presented.

11:30 Lunch on Own or Technology Workshop (Sponsorships Available)

NEXT GENERATION SEQUENCING - CASE STUDIES

1:00 Chair’s Remarks

1:05 Metagenomic Analyses of the Human Virome
Forest Rohwer, Ph.D., Biology Department, San Diego State University
Using uncultured techniques, we have shown that humans harbor a large number of previously undescribed viruses. Currently, we are determining if these viruses are found exclusively in humans or if they have non-human hosts. 

1:30 High-Throughput Computational Sequence Analysis
Rob Edwards, Ph.D., Biology Department, San Diego State University
As we approach the closing of the sequence of the 1,000 microbial genome, and sampling from more than 100 different environmental samples, new approaches for high-throughput annotation and interrogation of sequences are needed. The Subsystems approach to genome annotation provides the most accurate and consistent annotations, and provides a mechanism for statistical comparative metagenomics. The revolution in genome sequence data analysis is upon us.

1:55 Q&A for Case Study One

Case Study Two

2:05 Initial Experience with Medical Resequencing in Common, Complex Disorders
Stephen Kingsmore, Ph.D., President, National Center for Genome Resources 
Medical resequencing is a new approach to understanding the genetics of complex disorders. Medical resequencing refers to the brute-force sequencing of the genome or transcriptome of both affected and unaffected individuals or tissue samples. Dissection of the cause of common, complex traits is anticipated to have an immense impact on the biotechnology, pharmaceutical, diagnostics, healthcare and agricultural biotech industries. In particular, this approach should result in new diagnostic tests, identify novel targets for drug development, and reveal novel strategies for breeding improved crops. Medical resequencing is being made possible by the development of transformational, next generation genome sequencing instruments. We will review progress over the past year in two medical resequencing projects addressing common, complex disorders. Both projects involved the comprehensive resequencing of transcriptomes in small numbers of affected tissues of patients, cataloging and characterizing all nucleotide variants, prioritizing candidate genes and pathways, associating candidate genes with phenotypes in larger cohorts, and validating the findings in patient populations. 

2:30 Use of the Alpheus™ Sequence Variant Detection Software for Analysis of Medical Resequencing Data
Joann Mudge, Ph.D., Research Scientist, National Center for Genome Resources
Next-generation sequencing technologies enable comprehensive medical resequencing of common, complex disorders. Software systems for DNA sequence variant discovery that are based upon Sanger chemistry and base calling algorithms are not optimal for next generation technologies that feature relatively deep coverage, short read lengths, novel base calling and quality score determination methods, and relatively high error rates. The Alpheus™ Sequence Variant Detection software system includes an automatic data handling module, a computational analysis pipeline, a results database and a web-based query and visualization interface. Alpheus™ has been designed and implemented as a software-as-a-service application. The software was designed to mine large DNA sequence datasets for variants meeting user-specified criteria, such as transcript abundance, positional coverage, variant frequencies, and putative variant functional properties. We will demonstrate the use of Alpheus™ for novel data analyses in the context of two medical resequencing projects.

2:55 Q&A for Case Study Two

3:05 Refreshment Break (Last Chance for Poster and Exhibit Viewing)

3:30 Genomics of Organisms in the Wild
Eddy Rubin, M.D., Ph.D., Director, Joint Genome Institute, Lawrence Berkeley National Laboratories 
Metagenomics focuses on the sequence based analysis of organisms that are frequently inaccessible to standard laboratory approaches. This includes complex microbial communities that exist in nature but are resistant to growth under laboratory conditions to organisms that went extinct thousands of years ago. Several examples of metagenomics studies carried out at the DOE Joint Genome Institute will be presented.

3:55 Metagenome Sequence Data Management and Analysis
Victor Markowitz, Ph.D., Head, Biological Data Management Center, Lawrence Berkeley National Laboratories 
Studies of the collective genomes (also known as metagenomes) of environmental microbial communities (also known as microbiomes) are expected to lead to advances in environmental cleanup, agriculture, industrial processes, and alternative energy production. Similarly, studies of the metagenomes of human microbiomes will provide new insights into variations of microbial populations associated with the human body in health and disease, and will lead to the development of new treatment strategies. Metagenomes of specific microbiome samples are sequenced by organizations worldwide using different sequencing strategies, technology platforms, and annotation procedures. Metagenome data analysis is set in the context genome reference data and considers questions regarding composition and functional or metabolic potential of individual microbiomes, as well as differences between microbiome samples. Such analysis relies on efficient management of genome and metagenome data collected from multiple sources, while addressing sequencing technology differences and taking into account the iterative nature of sequence data generation and processing. Metagenome data management and analysis will be discussed in the context of IMG/M (http://img.jgi.doe.gov/m). IMG/M aims at providing support for comparative metagenome analysis in the integrated context of microbial genome and metagenome data generated with diverse technology platforms.

4:20 Q&A for Case Study Three

4:30 Panel Discussion with Afternoon Speakers

5:00 Close of Conference