FA 5 Progress Report WV-INBRE - Joan C. Edwards School of ...

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Program Director/Principal Investigator (Last, First, Middle): Rankin, Gary O 26completion of the work.Dr. Denvir was hired as an Assistant Professor in the Department of Biochemistry andMicrobiology at Marshall University in July 2011. He performs analysis of NGS datasets and assistin downstream pathway analyses. He is well acquainted with Casava, the software suite providedby Illumina for immediate data processing from the HiSeq 1000, and has attended training sessionsin the use of Tuxedo Suite software and CLC Genomics Workbench. The latter is currently beingtrialed by the Genomics Core, and the intention is to install and support use of this software in thenear future. Dr. Denvir also has expertise in MACS for analysis of Chip-Seq data and with IGV forthe visualization of analyzed data. He will continue to evaluate and select new analytical toolsneeded for NGS applications as these become available, develop new forms of analysis andconsult with investigators after the analysis is complete. He will work with MU Computing Servicesto ensure that our servers and storage devices are operating efficiently and have up to dateoperating systems.Dr. Boskovic develops protocols for NGS applications, prepare samples for NGS, operate theHiSeq1000 sequencer, perform routine maintenance of HiSeq sequencer and c-Bot cluster station,and manage raw data output. He examines and records quality metrics from all runs on theHisSeq1000. Dr. Boskovic continues to serve as microarray facility manager and perform sampleQCs, labeling, hybridization onto microarray slides, and microarray scanning. Dr Boskovic willadditionally provide pathway analysis on expression data sets. He insures that the HiSeq1000 andMicroarray scanner receive preventative maintenanceDr. Fan directs the operation of conventional DNA sequencing/genotyping, constructs NGS librariesand manages ACoRN genomic DNA banks. DNA sequencing, genotyping, and genomic DNAbanking are carried out by Dr. Fan and Jennifer Yu. Drs. Boskovic and Fan troubleshoot anyproblems with DNA/RNA extraction, NGS library construction, and microarray methods. Dr. Fanoversaw DNA sequencing and performed genotyping and LDLR gene sequencing related to theFamilial Combined Hyperlipidemia project (SPID #0026).Genomics Core Equipment: The Core is currently equipped with an Illumina HiSeq1000, a Linuxserver with 48 Terabytes for storage of sequencing data, 48 CPUs and 128GB memory, a Mac OSX Server with 12 CPUs, 6TB storage and 48GB memory, Agilent DNA Microarray Scanner, AgilentMicroarray Hybridization Station, two ABI Model 7000 Sequence Detection Systems (for RT PCR),one StepOnePlus Real Time PCR system, three Agilent 2100 Bioanalyzers (two of which handlehigh sensitivity DNA Chips), 1 Perkin Elmer, 2 Qubit and 2 NanoDrop spectrophotometers, AppliedBiosystems 3130 Genetic Analyzer, Luminex 100 system, 5 MJ/BioRad PTC200 Thermal Cyclers,1 Savant Speed Vac Concentrators and 1 Fast Prep FP120 Homogenizer. All instruments exceptthe FP120 are kept on service agreements. The Agilent Scanner has been upgraded to 2 micronresolution to allow for scanning of Agilent high density arrays (1.2 million features per array). TheABI3130 Genetic Analyzer (four capillary) can sequence 96 templates per day or ~500 STRgenotypes per day is sufficient for the needs of the WV-INBRE program and the university.Collaborations and Publications: The Genomics Core has a strong record of supporting thegenomic and statistical needs of statewide research programs and individual investigators. Thisincludes ongoing collaborations with the WV-INBRE and pending grant applications for the Centerfor Nutrition and Cancer and the WV Cancer Genomics Network.Table 1. Genomics Core Collaborations with funded/pending applicationsTitle: WV-INBRE Phase IIP.I.: Gary Rankin PhDAgency: NIH/NCRRRoles: D. Primerano, Director of Genomics Core and Appalachian Cardiovascular ResearchNetworkStatus: FundedPHS 2590 (Rev. 06/09)Continuation Format Page
Program Director/Principal Investigator (Last, First, Middle): Rankin, Gary O 27Title: West Virginia Cancer Genomics NetworkP.I. Richard Niles, PhD (MU)Agency: WV Division of Science and Research (Higher Education Policy Commission)Role: Donald Primerano, co-investigator and Director of NGS FacilityStatus: PendingTitle: COBRE Center For Nutrition and CancerP.I. Elaine Hardman, PhD (MU)Agency: NCRR/NIGMS NIHRole: Donald Primerano, co-investigator and Director of NGS FacilityStatus: PendingGenomics Core staff members have authored three publications and were acknowledged in twopublications in the past year.Publications1. Dementieva, Y., J. Denvir, L. Wei, D. A. Primerano, T. L. Green, P. Wehner, M. R. Flood, D.Calica, B. Freeman, M. Huff, S. Dodson, C. Hill, A. Francis, K. McIntyre, R. Kreisberg, S. Warren,H. Blackwood, M. Davis, H-M Lee. Identification of genes contributing to cardiovascular disease inoverweight and obese individuals from West Virginia. WV Medical Journal 108: 23-31 (2012)2. Varney, M. E., J. Buchanan, Y. Dementieva, W. E. Hardman, V. E. Sollars. A high omega-3 fattyacid diet has different effects on early and late stage myeloid progenitors. Lipids 46(1), 47-57(2011)3. Cieply, B., Riley, P., Pifer, P., Widmeyer, J., Addison, J., Ivanov, A., Denvir, J., Frisch, S.Suppression of the epithelial-mesenchymal transition by grainy head-like-2. Cancer Research,2012. In Press.Acknowledgments:1. Bhullar, J., and V. E. Sollars. YB-1 expression and function in early hematopoiesis.Immunogenetics 63, 337-350 (2011)2. Akinsete, J. A., G. Ion, T. R. Witte, W. E. Hardman. Consumption of high ω-3 fatty acid dietsuppressed prostate tumorigenesis in C3(1) Tag mice. Carcinogenesis. 33:140-8 (2012)Y11 usage: The Genomics Core provided the following services to WV-INBRE, COBRE, MU, andWVU during the reporting period (last column in the following table).2004-05 2005-06 2006-07 2007-08 2008-09 2009-10 2010-11 2011-PresTOTALAgilent Microarray (arrays/year) 54 100 41 80 188 320 112 40 935ABI 3130 (capillary sequencer) templates/year 480 1117 866 1294 1407 723 1614966 8467ABI Model 7000s and StepOnePlus (RT-PCR) runs/year 117 92 64 145 240 276283 88 1305Agilent Model 2100 Bioanalyzers (runs/year) 95 133 55 87 100 45 98 24 637Illumina HiSeq1000 (#runs/year) NA NA NA NA NA NA NA 6 6External Advising and Training:Dr. Ivana Yang, an established microarray investigator at the University of Colorado in Denvirand a member of the WV-INBRE External Advisory Committee, served as our external advisor onexperimental design and interpretation of data. She also advised in the selection of the IlluminaPHS 2590 (Rev. 06/09)Continuation Format Page
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FA 5 Progress Report WV-INBRE - Joan C. Edwards School of ...

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