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.
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.
|Orlow, I; Satagopan, J M; Berwick, M et al. (2015) Genetic factors associated with naevus count and dermoscopic patterns: preliminary results from the Study of Nevi in Children (SONIC). Br J Dermatol 172:1081-9|
|Carey, Bryce W; Finley, Lydia W S; Cross, Justin R et al. (2015) Intracellular ?-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature 518:413-6|
|Mosher, C E; Given, B A; Ostroff, J S (2015) Barriers to mental health service use among distressed family caregivers of lung cancer patients. Eur J Cancer Care (Engl) 24:50-9|
|Navi, Babak B; Reiner, Anne S; Kamel, Hooman et al. (2015) Association between incident cancer and subsequent stroke. Ann Neurol 77:291-300|
|Xu, Zhe; Wu, Chaochao; Xie, Fang et al. (2015) Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes. J Proteome Res 14:422-33|
|Xu, Hong; Cheng, Ming; Guo, Hongfen et al. (2015) Retargeting T cells to GD2 pentasaccharide on human tumors using Bispecific humanized antibody. Cancer Immunol Res 3:266-77|
|Gondo, Tatsuo; Poon, Bing Ying; Matsumoto, Kazuhiro et al. (2015) Clinical role of pathological downgrading after radical prostatectomy in patients with biopsy confirmed Gleason score 3 + 4 prostate cancer. BJU Int 115:81-6|
|Das, Sudeep; Thorek, Daniel L J; Grimm, Jan (2014) Cerenkov imaging. Adv Cancer Res 124:213-34|
|Fay, Allison; Glickman, Michael S (2014) An essential nonredundant role for mycobacterial DnaK in native protein folding. PLoS Genet 10:e1004516|
|Ripley, R Taylor; McMillan, Robert R; Sima, Camelia S et al. (2014) Second primary lung cancers: smokers versus nonsmokers after resection of stage I lung adenocarcinoma. Ann Thorac Surg 98:968-74|
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