Illumina Genome Analyzer II

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DESCRIPTION (provided by applicant): The overall objective of this proposal is to significantly enhance the capabilities of the established and highly successful Mount Sinai DNA Sequencing and Genotyping Shared Resource Facility (the DNAcore) by acquisition of a state-of-the-art Illumina Genome Analyzer II next-generation sequencer to support a broad array of genomics initiatives. This upgrade is critical to enable high-throughput, yet economical, genome-wide resequencing projects, as well as analyses of gene regulation, DNA genotype variation, and epigenetic modification, as they relate to understanding health and disease, and thus to maintain the DNAcore's ability to support Mount Sinai's over 300 NIH-funded researchers. The specific aims of this proposal are: 1) to upgrade the DNAcore facility from capillary electrophoresis-based sequencing and genotyping to include massively parallel sequencing by the Illumina Genome Analyzer II in order to maintain the facility's ability to provide rapid, reliable, economic, and now genome-wide, high-quality DNA sequencing; 2) to provide sample preparation, instrument operation and bioinformatics support to enable our investigators to make optimal use of the Illumina Genome Analyzer II to fulfill their DNA sequencing-based research needs; 3) to offer consultation support for the application-specific needs of our investigator's projects including ChIP-Seq, miRNA expression analyses, targeted resequencing, DNA methylation analyses, etc; and 4) to educate Mount Sinai researchers about the availability and use of next- generation sequencing to advantage their NIH-funded research. The success of this enhancement to the DNAcore's support of Mount Sinai investigators will be further assured by the strong cost-sharing commitment of the Institution (see Dean Dennis Charney's letter of support) to provide the additional funds needed to fully equip the DNAcore to optimally use the Illumina Genome Analyzer II through cost-sharing, to maintain the instrument, and to provide support for a dedicated FTE DNAcore associate to operate the instrument. RNA sample preparation support will be provided via Dr. Stuart Sealfon, Director of the Microarray, PCR and Bioinformatics Shared Resource Facility (see letter). In addition, the critical bioinformatics support required for effective analyses of the massive amounts of output data will be provided by a combination of resources from Mount Sinai's Computational Biology Shared Resource Center and Dr. Ravi Sachidanandam, a recent Faculty recruit from the Cold Spring Harbor Laboratory who has been supporting and developing Solexa bioinformatic tools to facilitate data manipulation and results visualization. PUBLIC HEALTH RELEVANCE: This application requests support to purchase an ultra-high capacity DNA sequencer, the Illumina Genome Analyzer II, that is required for new, sophisticated research techniques to define gene-based alterations which cause disease, to rapidly and economically sequence billions of nucleotides of critical small RNA and DNA samples, and to provide powerful new analyses of gene regulation and modification. Placement of this enabling "Next Generation" tool in the established Mount Sinai DNAcore, an Institution-wide Shared Resource Facility for DNA Sequencing, Genotyping and Synthesis, will permit studies not possible with the current sequencing equipment, vastly enriching the breadth and depth of sophisticated gene analyses in funded research projects designed to deal with critical issues of health and disease by our over 300 NIH-funded Investigators. These projects have the potential to dramatically improve society's ability to cope with an ever- expanding number of gene-based disorders, a wide variety of human cancers, environmental challenges to our genetic vulnerabilities, and rapidly evolving infectious diseases.