This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. GENE PROFILING CORE Working Group: I. DESCRIPTION DNA Sequencing Laboratory ?Dr. William Roth, Leader The DNA Sequencing laboratory is the longest-established lab in the Gene Profiling Core, having been established in the mid-1990's to provide DNA sequence analysis to MSM investigators involved in research utilizing molecular biology techniques. The lab uses capillary electrophoresis sequencing technology developed by Applied Biosystems (ABI) to resolve fluorescently-labeled DNA. The facility is built around the ABI 3130xl Gene Analyzer (16-capillary) and associated software for DNA sequence analysis. This platform enables the lab to offer both DNA sequence and fragment (microsatellite) analysis to research users. Software options for the sequencer allow enumeration of polymorphisms (SNPs) in patient samples, a service which can be used in conjunction with SNP discovery offered in the Human Genotyping Lab. The DNA Sequencing lab has DNA and protein sequence analysis software which is available to users. The lab also maintains a darkroom with an automated film processor for developing X-ray films and a large capacity shaker-incubator for growth of bacterial cultures, located adjacent to the darkroom. In addition, a digital image analyzer offers an alternative to the use of film for chemiluminescent imaging. Sequencing Lab Personnel: Dr. William W. Roth, Ph.D. Ms. Qi Yang, B.S. Technology Resources: Equipment: ABI 3130xl Gene Analyzer ABI 9600 thermocycler Kodak Model 2000A Film Processor New Brunswick Scientific Innova 4300 Shaker-Incubator Fuji LAS-4000 Luminescent Image Analyzer Software: ABI Suite: (Sequence Analysis 5.2, GeneMapper 4.0, SeqScape 2.5) Invitrogen Vector NTi10.3 suite Sequencer 4.2 Geneious 4.0.2 Molegro Virtual Docker 3.0 Human Genotyping Lab - Qing Song, Leader The Molecular Genetics Core Facility assists investigators to apply the genomic technologies to population-based genetic research. The strategic plan is to create a link between basic science, clinical investigation and population-based research by integrating genomic sciences into our research program. The central hypothesis is that health disparities are related in part to ethnicity-specific DNA variants in critical genes that influence the susceptibility to common diseases. Morehouse School of Medicine has a long-standing interest in the studies of ethnic disparities and a longstanding strength in community outreach to underserved minority populations. Accordingly, the major objective of the MSM Human Genome Core Laboratory is to enhance the research capacity on these sample cohorts and upgrade our research to the molecular genetics level based on cutting-edge genomic technologies. We currently provide service on the novel SNP discovery and SNP genotyping service, bioinformatics and general consultation on genetic study design. Gene Expression Lab ?Dr. Nerimiah Emmett, Leader The Genomic Core Facility continues to offer an integrated Genomic-based approach for basic research problems and clinical applications. With the establishment of CTSIA we will begin to integrated whole genome approaches to clinical problems for exploratory studies using micro array in the clinic for biomarker discovery;the development of biomarker footprints can have important clinical benefits for targeted therapeutics. We will push to make the faculty aware of the possibilities in future clinical applications. Our overall goal is to use discovery biomarkers as strong links between translational research and clinical development in individualized treatments. Upgrades to our existing equipment will be necessary this year to accommodate the new microarrays that will be available. The fundamental goal of the Gene Expression Laboratory at MSM is to provide an extensive, yet finite profile of the genes expressed in cells, tissues or organs at any given time. The defining benefit to MSM investigators will be to accelerated the research progress and contribute with respect to the identification of therapeutic targets. Micro array technology had its origin in the mid 1990's, with data produced from examination of a few specific syndromes;however, the technology is now applicable to virtually all new complex diseases. These genetic approaches to disease study began a new wave of investigation at MSM in 2001 with establishment of the Functional Genomics Core Laboratory based on the Agilent Technology. Currently, these techniques are used for basic research on microorganisms as well as the investigation of human disease states. The defining benefit of gene chip technology is derived from the enormous amount of relevant data that can be generated from a single experiment, thereby promising to accelerate the progress of individual research projects at an immeasurable rate. 1) TechnoloQV Resources: Agilent 2010 Bioanalyzer Agilent Scanner Micro array Agilent HP Bundle Workstation Bioanalyzer computers and associated software 2) Core Lab Personnel: Michelle Leander Bioinformatics Lab ?Dr. Leonard Anderson, Leader The bioinformatics suite was established at MSM in 2001 in order to provide enterprise level bioinformatics software solutions for investigators in basic, translational, and clinical research. At MSM we have co-developed computational biology to accomplish this objective at the same time as microarray technology has improved. Thus, the bioinformatics suite, located adjacent to the micro array core laboratory, facilitates analysis of gene expression data gathered from multiplatform microarrays (Agilent, Affymetrix, etc). In addition, Bioinformatics Lab personnel provide analysis and consultation related to gene expression and analysis of SNP data. Bioinformatics analysis includes, but is not limited to identification of genetic biomarkers and tangible diagnostic applications. 1) Technology Resources: Major Equipment Principal Components 1. Dell Storage Services 1. Gene Sifter 2. HP- Work Stations 2. Spotfire 3. Color Printers 3 Rosetta Luminator 4. 25 Server Computer Cluster 4. Ingenuity 5. Rosetta Application Server 5. Silicon Genetics 6. GeneSpring Application server 6. Affymetrix 7. Spotfire and Genesifter 7. Misc. Software Packages 8. Pathways 4 9. Array STAT 2) Core Lab Personnel Xing Hu
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