GENE PROFILING

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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. 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. Recent upgrades to instrumentation and software enable the lab to offer state-of the-art DNA 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 also 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. 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 on the studies of ethnic disparities and a longstanding strength on 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 Service Charges: DNA Sequencing Lab Service Cost DNA Sequencing: $6.00 /sequencing reaction (MSM) $8.00 /reaction (non-MSM) Large-user sequencing discount $5.00/reaction (MSM) (full 96-well plate) $6.00/reaction (non-MSM). DNA Fragment Analysis: $1.50 per sample (MSM) $2.00 per sample (non-MSM) Film processing: no charge for use of the processor Shaker-Incubator: no charge for use of the incubator Human Genotyping Lab We have just developed a service charge policy and price list, based on the information obtained from Emory University and University of Tennessee. However, due to the nature of this genetic variation core, it is more project-support core rather than a sample-based service; we are still in the developing stage on charging-back. At this stage, we have supported a number of researchers in their study design, proposal development, and grant submission. These users include, Drs. Bradford, Foreman, Meng, and Wang. Gene Expression Lab We have established competitive pricing for services offered by the Core Laboratory. Custom slides require at $4,000.00 set-up charge (one time) plus batches of slides at a cost which varies from $400.00 - $800.00 per slide. Note: customized slides can also be sold either by the investigator or by Agilent as a means to cover cost. The lab will work investigators to select appropriate technology for their needs. Micro array Services Cost Slides - Non Human $760.00 Slides - Human High Density $850.00 Slides  All Others $700.00 Slides  Customs Varies Other Services Cost RNA Storage Solutions $5.00/tube Collection of Tissues/Organs $30.00/hour RNA Isolation  cells $30.00 ea RNA Isolation  Tissues $45.00 ea RNA Quality checks/reports $30.00 DATA Reports/Samples FREE Training: Workshops, Lab Availability; $60.00/hour Inclusive of items above plus labor Bioinformatics Lab Bioinformatics service $60 / hour (consultation/training)