In this current age of genome biology, the primary objective of the Genomics Core is to accelerate the study of HIV and opportunistic infections associated with AIDS by providing researchers with access to genomic technologies. Examining host genetics following pathogen infection can identify new targets and pathways for drug development, reveal the genetic mechanisms of disease pathogenesis, determine predictive gene expression profiles that can guide treatment options, and identify single nucleotide polymorphisms (SNPs) associated with disease that can be used to judge the effectiveness of different antiviral drug therapies. To facilitate such research, the specific aims of the Genomics Core are as follows: (1) to provide researchers with a cost-effective mechanism to analyze mammalian gene expression at the whole genome level using microarray technology, (2) to enable the more precise quantification of both coding and non-coding gene expression using real-time quantitative RT-PCR (qRT-PCR), (3) to screen large numbers of samples for specific SNPs, and (4) to offer expertise and training in bioinformatics applications required to process and interpret the data generated by genomic technologies. The Genomics Core is currently outfitted with a suite of laboratory equipment to meet these aims (2 x ABI Prism 7700 Sequence Detection Systems, a Bio-Rad iCycler, an Affymetrix Fluidics Station 400 and a Sun Microsystems Sunfire 250 Enterprise server). Staff at the core are highly trained and skilled in areas of nucleic acid isolation, purification and quantification, and primer design, gene expression assays and bioinformatic analysis. In summary, the contribution of the Genomics Core to HIV- and AIDS-related research is best reflected by the numerous projects supported by the core, among which include the first assessment of HIV-stimulated gene expression in CD4 T cells, identification of pathways resulting in HIV induced apoptosis, the effects of methamphetamine use on HIV encephalitis, and identification of the amino acid polymorphisms that contribute to ritonavir hypersusceptibility. This proposal will allow the Genomics Core to continue bridging the gap between HIV-related research and genomic technologies in an economical manner. This will allow HIV research to benefit from the very latest developments in genome biology, which will ultimately translate into a better understanding of disease pathogenesis and the evolution of better therapies.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Center Core Grants (P30)
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Special Emphasis Panel (ZAI1)
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University of California San Diego
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