To maintain and build on the Sidney Kimmel Comprehensive Cancer Centers (SKCCC) record of excellence in the fields of cancer genetics and epigenetics, the SKCCC established a new Next Generation Sequencing Core (NGSC) as a shared resource in January 2009. A product of a convergence of advances in molecular biology, engineering, computer science, and bioinformatics. Next Generation Sequencing features the ability to sequence billions of base pairs of DNA in a single run, at a cost that is several orders of magnitude less than previous gold standard sequencing technologies. Next Generation Sequencing is an extremely versatile technology and can be used to investigate a multitude of genomic processes in a previously unimaginable genome-wide and unbiased fashion. In order to facilitate widespread adoption of this relatively new technology, rather than administering the Core as a """"""""black-box"""""""" facility, the Core operates as a """"""""collaborative Core"""""""" in which users can consult and collaborate with NGSC faculty and staff to: 1) identify the optimal molecular biology approaches (prior to sequencing library construction) to synapse their research questions with the capabilities of the Core, 2) prepare the appropriate libraries and carry out massively parallel sequencing, and 3) carry out the appropriate primary, secondary, and tertiary bioinformatics analyses to analyze and interpret the results. The NGSC features Applied Biosystems SOUD Next Generation Sequencing instruments capable of generating nearly 100 Gigabases of sequencing data in a single run, state-of-the-art equipment for sequencing library preparation and quality control, and powerful computational resources including a server with ten compute nodes (each containing Quad Core Intel Xeon processors and 16 Gigabytes of memory) and 100 terabytes of storage for dedicated bioinformatics analyses. The Core is currently administered by a faculty director overseeing all activities, a faculty Co-Director overseeing bioinformatics support, a laboratory manager, and a bioinformatics manager. The Core's goal is to be as flexible as possible in assisting researchers in exploring all aspects of cancer genetics and epigenetics, including, but not limited to, germline and somatic variation/mutation, genomic structural variations/alterations, transcriptome analysis, transcription factor binding sites, chromatin modifications, and DNA methylation. Lay: The Next Generation Sequencing Core provides cutting edge services that harness the most recent technological advances to allow large scale genomic sequencing of many hundreds of millions of DNA molecules in parallel at about 100,000 times less cost than previous sequencing technologies. These services are poised to rapidly accelerate the pace of discovery and clinical translation in cancer molecular genetics research. SKCCC Managed Shared Resource

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
2P30CA006973-49
Application #
8559655
Study Section
Subcommittee G - Education (NCI)
Project Start
2012-08-09
Project End
2017-04-30
Budget Start
2012-08-09
Budget End
2013-04-30
Support Year
49
Fiscal Year
2012
Total Cost
$229,477
Indirect Cost
$87,824
Name
Johns Hopkins University
Department
Type
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Isenberg, Sarina R; Lu, Chunhua; McQuade, John et al. (2017) Impact of a New Palliative Care Program on Health System Finances: An Analysis of the Palliative Care Program Inpatient Unit and Consultations at Johns Hopkins Medical Institutions. J Oncol Pract 13:e421-e430
Husain, Hatim; Velculescu, Victor E (2017) Cancer DNA in the Circulation: The Liquid Biopsy. JAMA 318:1272-1274
Holdhoff, Matthias; Cairncross, Gregory J; Kollmeyer, Thomas M et al. (2017) Genetic landscape of extreme responders with anaplastic oligodendroglioma. Oncotarget 8:35523-35531
Oh, Min-Hee; Collins, Samuel L; Sun, Im-Hong et al. (2017) mTORC2 Signaling Selectively Regulates the Generation and Function of Tissue-Resident Peritoneal Macrophages. Cell Rep 20:2439-2454
Klein, Orly R; Buddenbaum, Jessica; Tucker, Noah et al. (2017) Nonmyeloablative Haploidentical Bone Marrow Transplantation with Post-Transplantation Cyclophosphamide for Pediatric and Young Adult Patients with High-Risk Hematologic Malignancies. Biol Blood Marrow Transplant 23:325-332
Johnson 3rd, Burles A; Yarchoan, Mark; Lee, Valerie et al. (2017) Strategies for Increasing Pancreatic Tumor Immunogenicity. Clin Cancer Res 23:1656-1669
Antonarakis, Emmanuel S; Lu, Changxue; Luber, Brandon et al. (2017) Clinical Significance of Androgen Receptor Splice Variant-7 mRNA Detection in Circulating Tumor Cells of Men With Metastatic Castration-Resistant Prostate Cancer Treated With First- and Second-Line Abiraterone and Enzalutamide. J Clin Oncol 35:2149-2156
Cohen, Joshua D; Javed, Ammar A; Thoburn, Christopher et al. (2017) Combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancers. Proc Natl Acad Sci U S A 114:10202-10207
McCurdy, Shannon R; Kasamon, Yvette L; Kanakry, Christopher G et al. (2017) Comparable composite endpoints after HLA-matched and HLA-haploidentical transplantation with post-transplantation cyclophosphamide. Haematologica 102:391-400
Isella, Claudio; Brundu, Francesco; Bellomo, Sara E et al. (2017) Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer. Nat Commun 8:15107

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