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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Kurmi, Kiran; Hitosugi, Sadae; Yu, Jia et al. (2018) Tyrosine Phosphorylation of Mitochondrial Creatine Kinase 1 Enhances a Druggable Tumor Energy Shuttle Pathway. Cell Metab 28:833-847.e8
O'Mara, Tracy A; Glubb, Dylan M; Amant, Frederic et al. (2018) Identification of nine new susceptibility loci for endometrial cancer. Nat Commun 9:3166
Wallace, Sumer K; Halverson, Jessica W; Jankowski, Christopher J et al. (2018) Optimizing Blood Transfusion Practices Through Bundled Intervention Implementation in Patients With Gynecologic Cancer Undergoing Laparotomy. Obstet Gynecol 131:891-898
Shrestha, Shikshya; Zhang, Cheng; Jerde, Calvin R et al. (2018) Gene-Specific Variant Classifier (DPYD-Varifier) to Identify Deleterious Alleles of Dihydropyrimidine Dehydrogenase. Clin Pharmacol Ther 104:709-718
Hu, G; Dasari, S; Asmann, Y W et al. (2018) Targetable fusions of the FRK tyrosine kinase in ALK-negative anaplastic large cell lymphoma. Leukemia 32:565-569
Geller, James I; Fox, Elizabeth; Turpin, Brian K et al. (2018) A study of axitinib, a VEGF receptor tyrosine kinase inhibitor, in children and adolescents with recurrent or refractory solid tumors: A Children's Oncology Group phase 1 and pilot consortium trial (ADVL1315). Cancer 124:4548-4555
Luchtel, Rebecca A; Dasari, Surendra; Oishi, Naoki et al. (2018) Molecular profiling reveals immunogenic cues in anaplastic large cell lymphomas with DUSP22 rearrangements. Blood 132:1386-1398
Oishi, Naoki; Brody, Garry S; Ketterling, Rhett P et al. (2018) Genetic subtyping of breast implant-associated anaplastic large cell lymphoma. Blood 132:544-547
DuBois, Steven G; Mosse, Yael P; Fox, Elizabeth et al. (2018) Phase II Trial of Alisertib in Combination with Irinotecan and Temozolomide for Patients with Relapsed or Refractory Neuroblastoma. Clin Cancer Res 24:6142-6149
Farber, Benjamin A; Lalazar, Gadi; Simon, Elana P et al. (2018) Non coding RNA analysis in fibrolamellar hepatocellular carcinoma. Oncotarget 9:10211-10227

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