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Tuesday, June 9

7:00 am Registration and Morning Coffee

7:30 Breakfast Presentation Sponsored by  JMP Software
Next-Gen Biomarker Discovery Using Alpheus and JMP Genomics
Faye Schilkey, Associate Director, NM Genome Sequencing Center
Doug Robinson, Ph.D., JMP Genomics Application Scientist, SAS Institute Inc, JMP Division
Please join us for a complimentary breakfast seminar and learn how scientists at the National Center for Genome Resources (NCGR) have integrated JMP Genomics into their standard workflows for next-generation Illumina sequence analysis.  Co-presenters Faye Schilkey, Associate Director of NCGR’s New Mexico Genome Sequencing Center, and JMP Genomics Application Scientist Jordan Hiller will discuss cutting-edge NCGR research projects that display the flexibility and power of next-generation sequencing technology when combined with JMP Genomics tools for dynamic data analysis and pathway exploration.



8:15 Chairperson’s Remarks

Stephen Kingsmore, Ph.D., President and CEO, National Center for Genome Resources

8:20 Sequencing, Sequencing, and Sequencing

Wang Jun, Ph.D., Professor and Associate Director, Beijing Genomics Institute (BGI)

Breathtaking progress in DNA sequencing technology has made the costs drop and throughput increase at lightning speed. With more organisms including human sequenced, a flood of genetic data is being generated worldwide every day. Having a reference genome for certain organism becomes mundane and different strains are now being sequenced to discover variations related to a certain trait in that species. At the same time, large scale studies in exomics, metagenomics, epigenomics, and transcriptomics all become realistic suddenly. Scientists across many fields are utilizing these data for the development of better crops and livestock; for diagnostics, prognostics and therapies for cancer, neurological disorders and other complex diseases. BGI is on the cutting edge of translating genomics research into molecular breeding and disease association studies with belief that agriculture, medicine, drug development and clinical treatment would eventually enter a new stage with the understanding of genetic components of all the organisms.

8:50 Association Mapping Using Next-Gen Sequencing

Su Yeon Kim, Ph.D., Postdoctoral Scholar, Departments of Integrative Biology and Statistics, University of California, Berkeley

The price of DNA sequencing is falling so rapidly that direct sequencing is becoming a viable alternative to SNP genotyping in both candidate-gene and whole-genome association mapping studies. The optimal design of such studies depend on sequencing error rates, pooling efficacy in pooled studies, and other factors. This talk will introduce a new method for performing association mapping using direct sequencing and discuss several issues relating to choice of optimal strategy.

9:20 Fact or Fancy: $50,000 Analyzed, Individual Genomes in 2009

Stephen Kingsmore, Ph.D., President and CEO, National Center for Genome Resources

During the last six months there has been a dramatic decrease in the cost of individual genome sequencing, enabling the generation of sequence sets that far outstrip cost-effective analysis. Examples of current bottlenecks in analysis or individual genomes will be discussed. Progress at NCGR towards the $50,000 genome will be presented, such as hardware architecture for lightweight horizontal scalability, automation of repetitive analysis and validation tasks and minimization of effort to update and standardize reference resources.

9:50 Networking Coffee Break, Poster and Exhibit Viewing



Translating Small Genetic Contributions into Large Effects Using Phylogenetic Analyses

RosesAllen D. Roses, M.D., Professor of Medicine, Jefferson-Pilot Professor of Neurobiology and Genetics; Director, Deane Drug Discovery Institute; Senior Scholar, Fuqua School of Business; Member, Duke Institute for Genome Sciences & Policy; President of Shiraz Pharmaceuticals, Inc.






Multilocus Analysis of Sequence and Genotype Data

SchorkNicholas J. Schork, Ph.D., Director of Research, Scripps Genomic Medicine, Director of Biostatistics and Bioinformatics, The Scripps Translational Science, The Scripps Research Institute

Most diseases of contemporary public health concern, such as diabetes, hypertension, and cancer, are influenced by a number of genetic and non-genetic factors, each with small to moderate effect. Identifying genetic factors via genotyping and sequencing-based association strategies will thus be difficult if the combined effects of these genetic factors are not taken into consideration in a relevant association analyses. This talk will describe ways in which multilocus effects can be accommodated in association analysis strategies.

12:15 pm Close of Morning Session

12:30 Lunch on Your Own

1:30 Close of Meeting


Co-located Events: Translating Genomic Knowledge       The Business of Genomics         Genomic Sample Prep