This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.II. DESCRIPTIONDNA Sequencing Laboratory Dr. William Roth, LeaderThe 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 both instrumentation and software have enabled the lab to offer expanded DNA fragment (microsatellite) analysis to research users. In addition, 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 Sequencing lab also has computerized DNA and protein sequence analysis capabilities 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 ofbacterial cultures, located adjacent to the darkroom.Technology Resources:Instrumentation:Applied Biosystems 3130xl Gene AnalyzerApplied Biosystems 9600 thermocyclerKodak Model 2000A Film ProcessorNew Brunswick Scientific Innova 4300 Shaker-IncubatorSoftware:Applied Biosystems Suite: Sequence Analysis 5.2, GeneMapper 4.0, SeqScape 2.5Invitrogen Vector NTi10 suite, Sequencher 4.2Sequencing Lab PersonnelDr. William W. Roth, Ph.D.Ms. Qi Yang, B.S.Human Genotyping Lab - Qing Song, LeaderThe Molecular Genetics Core Facility assists investigators to apply the genomictechnologies to population-based 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-standinginterest 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 genetic level based on cutting-edge genomic technologies. We currently provide service on the novel SNP discovery and SNPgenotyping service.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 anextensive, 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 BioanalyzerAgilent Scanner Micro arrayAgilent HP Bundle WorkstationBioanalyzer computers and associated software2) Core Lab Personnel:Michelle LeanderBioinformatics Lab Dr. Leonard Anderson, leaderThe 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 Components1. Dell Storage Services 1. Gene Sifter2. HP- Work Stations 2. Spotfire3. Color Printers 3 Rosetta Luminator4. 25 Server Computer Cluster 4. Ingenuity5. Rosetta Application Server 5. Silicon Genetics6. GeneSpring Application server 6. Affymetrix7. Spotfire and Genesifter 7. Misc. Software Packages8. Pathways 49. Array STAT2) Core Lab PersonnelGuoshen Wang, PhD (Microarray/Bioinformatics)Xing Hu3)Service Charges:DNA Sequencing LabService CostDNA 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 processorShaker-Incubator: no charge for use of the incubatorHuman Genotyping LabWe 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. Welch, Bidulescu, Collins, Meng, Wang, Song, Newman, Lyn in Morehouse School of Medicine, and Drs. Taylor and Zafari in Emory University.Gene Expression LabWe 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 CostSlides - Non Human $760.00Slides - Human High Density $850.00Slides All Others $700.00Slides Customs VariesOther Services CostRNA Storage Solutions $5.00/tubeCollection of Tissues/Organs $30.00/hourRNA Isolation cells $30.00 eaRNA Isolation Tissues $45.00 eaRNA Quality checks/reports $30.00DATA Reports/Samples FREETraining: Workshops, Lab Availability; $60.00/hourInclusive of items above plus laborBioinformatics LabBioinformatics service $60 / hour (consultation/training)
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