A new generation of ultra high-throughput DNA sequencers is transforming biomedical research. These instruments provide a wide range of applications to basic and clinical research, including SNP discovery, analysis of transcriptome profiles, identification of protein:DNA interactions and hypersensitive sites, and characterization of methylation and chromatin marks at the whole-genome scale. This proposal seeks funds to expand instrumentation within Duke University's Genome Sequencing &Analysis Core Facility by adding a HiSeq" 2000 System next-generation DNA sequencer manufactured by Illumina. Existing next-generation capabilities within the Core Facility include four short-read instruments (three Illumina GAII" and one Applied Biosystems SOLiD" 4) and one long-read instrument (Roche GS-FLX"). We acquired our first GAII" three years ago and replacing this instrument with the new HiSeq" 2000 would substantially expand capacity to meet growing demand and extend the range of services that the Core Facility provides to researchers. The HiSeq" platform offers both a substantially larger throughput and a faster run time. Access to this instrument will therefore save some research projects time and cost, and provide others with expanded information. This instrument will be primarily utilized by eight identified Duke investigators for diversity of ongoing projects. Because of a pre-existing strong Illumina user base in the Core Facility and the HiSeq" versatility, we anticipate that this new instrument will enable a wide range of additional projects over its lifetime. Efficient utilization of the instrument is ensured y placement in a Core Facility with a proven record of accomplishment of more than a decade of support for research projects. Since this new instrument would replace an older Illumina instrument, its integration to an established workflow would be easily achieved and no additional ancillary equipment, staff, and computing infrastructure would be required. The Core Facility provides start-to- finish partnership with investigators that includes consultation, sample preparation, library construction, DNA sequencing, post-run quality control, and in-depth bioinformatics and statistical analyses. A team of technicians and bioinformaticians with strong experience in operating various next-generation DNA sequencers would support the new instrument, allowing non-specialists to take immediate advantage of its capabilities. A HiSeq" 2000 DNA sequencer would provide substantial benefit to several ongoing NIH-funded projects and serve as a valuable catalyst for additional projects throughout Duke University's vibrant biomedical research community.