The Genome Analysis Shared Resource (GEN) provides Mayo Clinic Cancer Center (MCCC) members efficient, high-quality, cost-effective access to state-of-the-art genomics technologies for studying gene structure and function. Since 2003, the GEN components have been working in a coordinated fashion to provide technical expertise, instrumentation, and comprehensive support for nucleic acid sequencing, gene expression profiling, and genotyping. Support for NextGen sequencing and gene expression regulation through RNAi analysis were added in 2007. The services provided by the facility include deep sequencing studies of RNA and DNA on Illumina NovaSeq, HiSeq and MiSeq instruments, and Pacific Biosciences Single Molecule Real Time Sequencing on the new Sequel platform. In addition, we offer full-service genotyping and gene transcript analysis using Affymetrix Genechip? technology and Illumina BeadChips. Methylation analyses are offered using Illumina methylation arrays and reduced representational bisulfite sequencing on Illumina HiSeq instruments. An important additional capability is offered by the RNA Interference shared resource, which provides special contract pricing on packaging reagents for lentiviral production and access to the complete Open Biosystems pGIPZ knockdown library to all Mayo Clinic investigators. Each of the 4 areas of focus (Sequencing, Gene Expression, Genotyping and RNA Interference) is directed by a senior staff-level Associate Director with expertise in the area of focus. With significant institutional support, we have continued to add new instruments, personnel and services in support of MCCC activities. There is a well-developed cooperative administrative structure that oversees our activities and ensures timely access and affordable pricing to MCCC members. All of our activities are data intensive, and we interact closely with the IT and bioinformatics resources to meet the needs of our users, from project inception through the final delivery of data. Since the last competitive grant renewal, more than 158 MCCC members from the 10 Programs and all 3 MCCC sites have used the services offered by the GEN and MCCC projects account for about half of all the activity in the GEN. The value of this resource to the MCCC is highlighted by the large number of high-quality, peer-reviewed publications that were based upon data produced in our facilities.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
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Subcommittee I - Transistion to Independence (NCI)
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Mayo Clinic, Rochester
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Lu, Yingchang; Beeghly-Fadiel, Alicia; Wu, Lang et al. (2018) A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk. Cancer Res 78:5419-5430
Dasari, Surendra; Newsom, Sean A; Ehrlicher, Sarah E et al. (2018) Remodeling of skeletal muscle mitochondrial proteome with high-fat diet involves greater changes to ?-oxidation than electron transfer proteins in mice. Am J Physiol Endocrinol Metab 315:E425-E434
Nowsheen, Somaira; Aziz, Khaled; Aziz, Asef et al. (2018) L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage. Nat Cell Biol 20:455-464
Razidlo, Gina L; Burton, Kevin M; McNiven, Mark A (2018) Interleukin-6 promotes pancreatic cancer cell migration by rapidly activating the small GTPase CDC42. J Biol Chem 293:11143-11153
Wu, Dongyan; Yang, Haitao; Winham, Stacey J et al. (2018) Mediation analysis of alcohol consumption, DNA methylation, and epithelial ovarian cancer. J Hum Genet 63:339-348
Leon-Ferre, Roberto A; Polley, Mei-Yin; Liu, Heshan et al. (2018) Impact of histopathology, tumor-infiltrating lymphocytes, and adjuvant chemotherapy on prognosis of triple-negative breast cancer. Breast Cancer Res Treat 167:89-99
Jahanseir, Khadijeh; Xing, Deyin; Greipp, Patricia T et al. (2018) PDGFB Rearrangements in Dermatofibrosarcoma Protuberans of the Vulva: A Study of 11 Cases Including Myxoid and Fibrosarcomatous Variants. Int J Gynecol Pathol 37:537-546
Painter, Jodie N; O'Mara, Tracy A; Morris, Andrew P et al. (2018) Genetic overlap between endometriosis and endometrial cancer: evidence from cross-disease genetic correlation and GWAS meta-analyses. Cancer Med 7:1978-1987
Yu, Jia; Qin, Bo; Moyer, Ann M et al. (2018) DNA methyltransferase expression in triple-negative breast cancer predicts sensitivity to decitabine. J Clin Invest 128:2376-2388
Sugihara, Takaaki; Werneburg, Nathan W; Hernandez, Matthew C et al. (2018) YAP Tyrosine Phosphorylation and Nuclear Localization in Cholangiocarcinoma Cells Are Regulated by LCK and Independent of LATS Activity. Mol Cancer Res 16:1556-1567

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