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.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA008748-51
Application #
9204777
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
Livshits, Geulah; Alonso-Curbelo, Direna; Morris 4th, John P et al. (2018) Arid1a restrains Kras-dependent changes in acinar cell identity. Elife 7:
Sheckter, Clifford C; Panchal, Hina J; Razdan, Shantanu N et al. (2018) The Influence of Physician Payments on the Method of Breast Reconstruction: A National Claims Analysis. Plast Reconstr Surg 142:434e-442e
Yamazaki, Takashi; Liu, Lizhi; Lazarev, Denis et al. (2018) TCF3 alternative splicing controlled by hnRNP H/F regulates E-cadherin expression and hESC pluripotency. Genes Dev 32:1161-1174
Spaliviero, Massimiliano; Power, Nicholas E; Murray, Katie S et al. (2018) Intravenous Mannitol Versus Placebo During Partial Nephrectomy in Patients with Normal Kidney Function: A Double-blind, Clinically-integrated, Randomized Trial. Eur Urol 73:53-59
I??k, Mehtap; Levorse, Dorothy; Rustenburg, Ariën S et al. (2018) pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. J Comput Aided Mol Des 32:1117-1138
Rajshekar, Srivarsha; Yao, Jun; Arnold, Paige K et al. (2018) Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. Elife 7:
Aherne, Emily A; Pak, Linda M; Goldman, Debra A et al. (2018) Intrahepatic cholangiocarcinoma: can imaging phenotypes predict survival and tumor genetics? Abdom Radiol (NY) 43:2665-2672
Wolner, Z J; Bajaj, S; Flores, E et al. (2018) Variation in dermoscopic features of basal cell carcinoma as a function of anatomical location and pigmentation status. Br J Dermatol 178:e136-e137
Rieth, Elizabeth F; Fischer, Gregory W; Afonso, Anoushka M (2018) Organization of Multidisciplinary Cancer Care for the Surgical Patient: Role of Anesthesiologists. Curr Anesthesiol Rep 8:368-374
Patel, Seema; Wang, Shiyang; Snuderl, Matija et al. (2018) Pre-treatment lymphopenia and indication of tumor-induced systemic immunosuppression in medulloblastoma. J Neurooncol 136:541-544

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