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. II. DESCRIPTION A. 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-1990s 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 instrument and Genemapper software have enabled the lab to offer DNA fragment (microsatellite) analysis to research users. SeqScape software allows enumeration of polymorphisms (SNPs) in patient samples, which can be used in conjunction with SNP discovery offered in the Human Genotyping Lab. The Sequencing lab also has additional DNA and protein sequence analysis capabilities and maintains an automated film processor for developing X-ray films and a large capacity shaker-incubator for growth of bacterial cultures (located adjacent to darkroom). 1) Technology Resources: Instrumentation: Applied Biosystems 3130xl Gene Analyzer, ABI 9600 thermocycler Kodak Model 2000A Film Processor New Brunswick Scientific Innova 4300 Shaker-Incubator Software: Applied Biosystems Suite: Sequence Analysis 5.2, GeneMapper 4.0, SeqScape 2.5 Invitrogen Vector NTi10 suite, Sequencher 4.2, ClustalX 2) Core Lab Personnel Ms. Qi Yang, Lab Technician 3) Services Offered and Fee Structure 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 B. Human Genotyping Laboratory - Dr. Qing Song, leader Ethnic disparities in common disease are related to a complex interplay between social-cultural, genetic and environmental factors. The long-term objective of the Human Genome Core Laboratory is to enhance the research capacity of the institution to incorporate genomic research into its translational research programs, especially research relevant to ethnic disparities in health. 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. One of the major challenges for investigators who intend to incorporate genetic markers in the study of ethnic populations is the lack of genomic reagents that are appropriately designed for use in different ethnic populations. The major objective of the MSM RCMI Human Genotyping Core Laboratory is to enhance the research capacity related to these sample cohorts based on cutting-edge genomic technologies. Toward this end, our intention is to: 1) establish the research infrastructure necessary to pursue molecular epidemiologic studies of ethnic disparities of human diseases; 2) provide services to conduct genetic epidemiological studies in various ethnic populations, including high-throughput genotyping, comprehensive SNP database searches, haplotype analysis and linkage disequilibrium block (LD) analysis, and TagSNP selection, as well as data interpretation; and 3) provide consultation and education to the MSM research community. The Genotyping laboratory provides novel SNP discovery, high throughput genotyping, comprehensive SNP database search and associated haplotype analysis, as well as genome linkage disequilibrium block structure configuration on candidate genes. The lab also provides consultation and education in molecular genetics. 1) Technology Resources: Transgenomics DHPLC-WAVE system Biotage PSQ96MA pyrosequencing genotyping platform 2) Core Lab Personnel Weinian Rao, BS Dong Li, MD, PhD 3) Services Offered and Fee Structure Service Cost Pyrosequencing / SNP genotyping $1.00 / sample, plus an assay setup fee $200.00 / assay. WAVE /SNP discovery $ 5000 for 5000 bp / 24 samples Bioinformatics service $60 / hour (consultation/training) (Includes database SNP, LD analysis, haplotype analysis, TagSNP selection) C. Gene Expression Laboratory - Dr. Nerimiah Emmett, leader 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 accelerate the research progress and contribute with respect to the identification of therapeutic targets. Microarray technology had its origin in the mid 1990s, with data produced from examination of a few specific syndromes; however the technology is now applicable to virtually all 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) Technology Resources: Agilent 2100 Bioanalyzer Agilent Scanner Micro array Agilent H.P. Bundle Work station Bioanalyzer computers and associated software 2) Core Lab personnel Guoshen Wang, PhD (Microarray/Informatics) 3) Services Offered and Fee Structure We have established competitive pricing for services offered by the core laboratory. Custom slides require a $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 recover cost. The lab will work with investigators to select appropriate technology for their needs. Microarray Services Cost Slides-Non Human $760.00 Slides-Human- High Density $850.00 Slides- All Others $700.00 Slides-Custom $ Varies Other Services/Products Cost 1. RNA Storage Solutions $ 5.00/ tube 2. Collection of Tissues/Organs $ 30.00/ hour 3. RNA Isolation-cells $30.00 ea 4. RNA Isolation-Tissues $45.00 ea 5. RNA Quality checks/ Report $30.00 ea 6. DATA Reports/ Samples $ FREE 7. Training: Workshops, Laboratory Availability; Inclusive of items above plus labor $60.00/hr. D. Bioinformatics Laboratory  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 multi-platform 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 Guoshen Wang, PhD (Microarray/Bioinformatics) Xing Hu 3) Services Offered and Fee Structure Service Cost Bioinformatics service $60 / hour (consultation/training)