The Bioinformatics Core was created to provide and build bioinformatics services and infrastructure for the MSKCC research community. The services of the core include scientific consultations, high performance computing and high capacity data storage support, training via clinics and workshops, custom programming on both small and large scale software projects, and pipelines for data analysis. The Core has grown to 13 full time staff members including PhD level research scientists and a professional staff of engineers, programmers and systems administrators. The Core provides all levels of bioinformatics support from small scale script writing to long term analytic support. As new technologies emerge, such as next-generation sequencing, the Core's focus and services have grown to meet them. The broad range of services and collaborative work provided by the Bioinformatics Core has supported the research of 66 investigators in the past year. During the past grant period the work of the Core has contributed to 365 publications of researchers from 8 research programs. For example, the Core supported Drs. Sawyers, Gerald, and Sander in the analysis of genomic datasets generated by the MSKCC Genomics Core from 214 primary and metastatic prostate cancer samples that were obtained from the MSKCC Pathology Core. The Core developed the informatics pipeline for analysis of exon resequencing data, generated plots of copy number alterations from array CGH data, and conducted preliminary analyses of the mRNA transcriptome and microRNA expression data from arrays run by the Genomics Core. This work led to the first comprehensive integrated genomic analysis of prostate cancer and has served as a key source of information for the field since its publication in 2010.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA008748-51
Application #
9204776
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
2017-01-01
Budget End
2017-12-31
Support Year
51
Fiscal Year
2017
Total Cost
Indirect Cost
Name
Sloan-Kettering Institute for Cancer Research
Department
Type
DUNS #
064931884
City
New York
State
NY
Country
United States
Zip Code
10065
Schlappe, Brooke A; Weaver, Amy L; Ducie, Jennifer A et al. (2018) Multicenter study comparing oncologic outcomes between two nodal assessment methods in patients with deeply invasive endometrioid endometrial carcinoma: A sentinel lymph node algorithm versus a comprehensive pelvic and paraaortic lymphadenectomy. Gynecol Oncol 151:235-242
Pareja, Fresia; Da Cruz Paula, Arnaud; Murray, Melissa P et al. (2018) Recurrent MED12 exon 2 mutations in benign breast fibroepithelial lesions in adolescents and young adults. J Clin Pathol :
Yao, Zhan; Gao, Yijun; Su, Wenjing et al. (2018) RAF inhibitor PLX8394 selectively disrupts BRAF dimers and RAS-independent BRAF-mutant-driven signaling. Nat Med :
Dumane, Vishruta A; Saksornchai, Kitwadee; Zhou, Ying et al. (2018) Reduction in low-dose to normal tissue with the addition of deep inspiration breath hold (DIBH) to volumetric modulated arc therapy (VMAT) in breast cancer patients with implant reconstruction receiving regional nodal irradiation. Radiat Oncol 13:187
Turashvili, Gulisa; Fix, Daniel J; Soslow, Robert A et al. (2018) Wilms Tumor of the Ovary: Review of the Literature and Report of 2 Cases. Int J Gynecol Pathol :
Krantz, Benjamin A; O'Reilly, Eileen M (2018) Biomarker-Based Therapy in Pancreatic Ductal Adenocarcinoma: An Emerging Reality? Clin Cancer Res 24:2241-2250
Chowell, Diego; Morris, Luc G T; Grigg, Claud M et al. (2018) Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy. Science 359:582-587
Morgani, Sophie M; Metzger, Jakob J; Nichols, Jennifer et al. (2018) Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning. Elife 7:
Senders, Max L; Que, Xuchu; Cho, Young Seok et al. (2018) PET/MR Imaging of Malondialdehyde-Acetaldehyde Epitopes With a Human Antibody Detects Clinically Relevant Atherothrombosis. J Am Coll Cardiol 71:321-335
Fang, Jing; Muto, Tomoya; Kleppe, Maria et al. (2018) TRAF6 Mediates Basal Activation of NF-?B Necessary for Hematopoietic Stem Cell Homeostasis. Cell Rep 22:1250-1262

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