In January 2012, the CCSG-supported Genomics and DNA Analysis facilities consolidated their activities to form a comprehensive institutional genomics shared resource: the Sequencing and Microarray Facility (SMF). The mission of the SMF is to support genomics research at MD Anderson by providing investigators with access to state-of-the-art instrumentation and a high level of technical expertise in a centralized facility, thereby minimizing the duplication of expensive equipment while maintaining technical excellence. The SMF, located in a newly renovated 1600-square-foot laboratory space, provides a complete range of genomic services that includes project and technology consultation, RNA and DNA quality assessment and quantification, Sanger DNA sequencing, comprehensive lllumina next-generation sequencing services, gene resequencing, fluorescent fragment analysis, and TaqMan-based gene expression analysis. The SMF also provides complete DNA and RNA services for several microarray applications, including gene expression, single-nucleotide polymorphism, comparative genomic hybridization, chromatin immunoprecipitation microarrays, and microRNA profiling. MD Anderson has demonstrated its support and commitment to the SMF by providing more than $1.2 million in funding for the purchase of state-of-the-art instrumentation. Major equipment includes AB 3730 sequencers, lllumina Hiseq2000 sequencers, an AB 7900 Sequence Detection System, Affymetrix GeneChip systems, an Axon Genepix 4000B Scanner, a MAUI Hybridization System, and an lllumina BeadXpress and iScan. Since 2008, the SMF component facilities processed 785,638 samples for 399 Pis in 19 CCSG programs supporting 14 P01, 227 R01, and 14 SPORE grants. The total number of samples processed increased 39%, and the number of Pis using the SMF increased 32% over the previous grant period (3/1/02-2/28/07). Publications cited using the SMF have appeared in several high impact journals including Nat Genet, Lancet Oncol, Cell and Cancer Cell. Peer-reviewed Pis accounted for 96% of the samples processed. Funding for the new grant cycle is proposed to come from the CCSG (22%), user fees (77.8%) and institutional support (0.2%). Future plans include the expansion of the NGS service to include platforms for midscale and single-molecule sequencing. The SMF will continue to expand the range of NGS and validation services offered and develop methods that can successfully use MD Anderson's unique resource of archival tumor samples.
The SMF is the primary sequencing and microarray facility of MD Anderson. The SMF provides essential genomic analysis services to support cancer center members in basic science, translational, and population based research programs. Addition of essential whole genome and whole transcriptome sequencing services has enabled researchers to do more exploratory biomarker experiments.
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