The Genomics Core Lab (GCL) is a full-service microarray analysis and sequencing facility. The Core supports basic, translational and clinical research by providing DNA and RNA analysis services from experimental design and sample preparation to basic data analysis and training. Sample preparation services include RNA and DNA extraction from standard and challenging sources as well as sample quality control assessment. The functional genomics applications available are gene expression, array Comparative Genomic Hybridization (aCGH), microRNA, SNP, Chromatin Immunoprecipitation and methylation analysis measured with Affymetrix, lllumina or Agilent microarrays. Microarray validation by Real-Time PCR is also provided. In 2006, the GCL expanded its portfolio of measurement technologies to include Sanger sequencing as well as several Next Generation Sequencing platforms, the PGM from lon Torrent, two HiSeq2000 and a MiSeq from lllumina, a 454FLX and a 454Junior from Roche and two SOLiD5500 from Life Technologies. The availability of these different sequencing technologies enables high-throughput analysis Of a range of genomics applications, such as variant detection, epigenomics, transcriptome sequencing and more. GCL staff also provides basic bioinformatics analysis, training and support. The broad range of services provided by the Genomics Core has supported the research of 129 Investigators in/the past year. During the past grant period the work of the Core has contributed to 484 publications of researchers from 9 research programs. The Genomics Core was chosen as one of the Cancer Genome Characterization Centers and generated Agilent CGH data for 832 glioblastoma multiforme, 1179 ovarian serous cystadenocarcinomas and 244 lung adenocarcinomas. The performance and contribution of the MSKCC TCGA team (clinicians, scientists, computational biologists and genomicists) during the pilot phase helped the Institution obtain a spot in the actual TCGA project that started in 2009, as a Genome Data Analysis center.

Public Health Relevance

The Genomics Core provides a broad range of services and expertise to Center investigators interested in evaluating gene expression, chromosome structure, and nucleotide sequence at a wide genome scale. Given the importance of genomic applications to cancer research, the Core will continue to remain essential For the basic, translational, and clinical research mission of the center.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
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Subcommittee G - Education (NCI)
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Shafik, Hasnaa
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Sloan-Kettering Institute for Cancer Research
New York
United States
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Steuer, Conor E; Behera, Madhusmita; Berry, Lynne et al. (2016) Role of race in oncogenic driver prevalence and outcomes in lung adenocarcinoma: Results from the Lung Cancer Mutation Consortium. Cancer 122:766-72
Dominguez-Rosado, Ismael; Moutinho Jr, Vitor; DeMatteo, Ronald P et al. (2016) Outcomes of the Memorial Sloan Kettering Cancer Center International General Surgical Oncology Fellowship. J Am Coll Surg 222:961-6
Iasonos, Alexia; O'Quigley, John (2016) Integrating the escalation and dose expansion studies into a unified Phase I clinical trial. Contemp Clin Trials 50:124-34
Ulaner, Gary A; Hyman, David M; Ross, Dara S et al. (2016) Detection of HER2-Positive Metastases in Patients with HER2-Negative Primary Breast Cancer Using 89Zr-Trastuzumab PET/CT. J Nucl Med 57:1523-1528
Brown, Anna M; Nagala, Sidhartha; McLean, Mary A et al. (2016) Multi-institutional validation of a novel textural analysis tool for preoperative stratification of suspected thyroid tumors on diffusion-weighted MRI. Magn Reson Med 75:1708-16
Akkari, Leila; Gocheva, Vasilena; Quick, Marsha L et al. (2016) Combined deletion of cathepsin protease family members reveals compensatory mechanisms in cancer. Genes Dev 30:220-32
Theilen, Till M; Chou, Alexander J; Klimstra, David S et al. (2016) Esophageal Adenocarcinoma and Squamous Cell Carcinoma in Children and Adolescents: Report of 3 Cases and Comprehensive Literature Review. J Pediatr Surg Case Rep 5:23-29
Robinson, June K; Halpern, Allan C (2016) Cost-effective Melanoma Screening. JAMA Dermatol 152:19-21
Calzavara-Pinton, Pier Giacomo; Rossi, Maria Teresa; Zanca, Arianna et al. (2016) Oral Polypodium leucomotos increases the anti-inflammatory and melanogenic responses of the skin to different modalities of sun exposures: a pilot study. Photodermatol Photoimmunol Photomed 32:22-7
Ripley, R Taylor; Suzuki, Kei; Tan, Kay See et al. (2016) Postinduction positron emission tomography assessment of N2 nodes is not associated with ypN2 disease or overall survival in stage IIIA non-small cell lung cancer. J Thorac Cardiovasc Surg 151:969-77, 979.e1-3

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