Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

被引:252
作者
Ellis, Matthew J. [1 ]
Gillette, Michael [3 ]
Carr, Steven A. [3 ]
Paulovich, Amanda G. [4 ]
Smith, Richard D. [5 ]
Rodland, Karin K. [5 ]
Townsend, R. Reid [2 ]
Kinsinger, Christopher [6 ]
Mesri, Mehdi [6 ]
Rodriguez, Henry [6 ]
Liebler, Daniel C. [7 ]
机构
[1] Washington Univ, Sch Med, Dept Med, Div Oncol, St Louis, MO 63110 USA
[2] Washington Univ, Sch Med, Dept Med, Div Endocrinol & Metab, St Louis, MO 63110 USA
[3] Broad Inst MIT & Harvard, Cambridge, MA USA
[4] Fred Hutchinson Canc Res Ctr, Seattle, WA 98104 USA
[5] Pacific NW Natl Lab, Div Biol Sci, Richland, WA 99352 USA
[6] NCI, Off Canc Clin Prote Res, NIH, Bethesda, MD 20892 USA
[7] Vanderbilt Ingram Canc Ctr, Jim Ayers Inst Canc Detect & Diag, Nashville, TN USA
关键词
CELL-LINES; QUANTIFICATION; PROTEINS;
D O I
10.1158/2159-8290.CD-13-0219
中图分类号
R73 [肿瘤学];
学科分类号
100214 [肿瘤学];
摘要
The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods. (C) 2013 AACR.
引用
收藏
页码:1108 / 1112
页数:5
相关论文
共 20 条
[1]
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma [J].
Addona, Terri A. ;
Abbatiello, Susan E. ;
Schilling, Birgit ;
Skates, Steven J. ;
Mani, D. R. ;
Bunk, David M. ;
Spiegelman, Clifford H. ;
Zimmerman, Lisa J. ;
Ham, Amy-Joan L. ;
Keshishian, Hasmik ;
Hall, Steven C. ;
Allen, Simon ;
Blackman, Ronald K. ;
Borchers, Christoph H. ;
Buck, Charles ;
Cardasis, Helene L. ;
Cusack, Michael P. ;
Dodder, Nathan G. ;
Gibson, Bradford W. ;
Held, Jason M. ;
Hiltke, Tara ;
Jackson, Angela ;
Johansen, Eric B. ;
Kinsinger, Christopher R. ;
Li, Jing ;
Mesri, Mehdi ;
Neubert, Thomas A. ;
Niles, Richard K. ;
Pulsipher, Trenton C. ;
Ransohoff, David ;
Rodriguez, Henry ;
Rudnick, Paul A. ;
Smith, Derek ;
Tabb, David L. ;
Tegeler, Tony J. ;
Variyath, Asokan M. ;
Vega-Montoto, Lorenzo J. ;
Wahlander, Asa ;
Waldemarson, Sofia ;
Wang, Mu ;
Whiteaker, Jeffrey R. ;
Zhao, Lei ;
Anderson, N. Leigh ;
Fisher, Susan J. ;
Liebler, Daniel C. ;
Paulovich, Amanda G. ;
Regnier, Fred E. ;
Tempst, Paul ;
Carr, Steven A. .
NATURE BIOTECHNOLOGY, 2009, 27 (07) :633-U85
[2]
Phosphoproteomics Identifies Driver Tyrosine Kinases in Sarcoma Cell Lines and Tumors [J].
Bai, Yun ;
Li, Jiannong ;
Fang, Bin ;
Edwards, Arthur ;
Zhang, Guolin ;
Bui, Marilyn ;
Eschrich, Steven ;
Altiok, Soner ;
Koomen, John ;
Haura, Eric B. .
CANCER RESEARCH, 2012, 72 (10) :2501-2511
[3]
Quantification of β-Catenin Signaling Components in Colon Cancer Cell Lines, Tissue Sections, and Microdissected Tumor Cells using Reaction Monitoring Mass Spectrometry [J].
Chen, Yi ;
Gruidl, Mike ;
Remily-Wood, Elizabeth ;
Liu, Richard Z. ;
Eschrich, Steven ;
Lloyd, Mark ;
Nasir, Aejaz ;
Bui, Marilyn M. ;
Huang, Emina ;
Shibata, David ;
Yeatman, Timothy ;
Koomen, John M. .
JOURNAL OF PROTEOME RESEARCH, 2010, 9 (08) :4215-4227
[4]
The Genomic Landscape of Breast Cancer as a Therapeutic Roadmap [J].
Ellis, Matthew J. ;
Perou, Charles M. .
CANCER DISCOVERY, 2013, 3 (01) :27-34
[5]
Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer [J].
Gallien, Sebastien ;
Duriez, Elodie ;
Crone, Catharina ;
Kellmann, Markus ;
Moehring, Thomas ;
Domon, Bruno .
MOLECULAR & CELLULAR PROTEOMICS, 2012, 11 (12) :1709-1723
[6]
METHOD OF THE YEAR Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry [J].
Gillette, Michael A. ;
Carr, Steven A. .
NATURE METHODS, 2013, 10 (01) :28-34
[7]
Molecular Pathways: Extracting Medical Knowledge from High-Throughput Genomic Data [J].
Goldstein, Theodore C. ;
Paull, Evan O. ;
Ellis, Matthew J. ;
Stuart, Joshua M. .
CLINICAL CANCER RESEARCH, 2013, 19 (12) :3114-3120
[8]
GeLC-MRM Quantitation of Mutant KRAS Oncoprotein in Complex Biological Samples [J].
Halvey, Patrick J. ;
Ferrone, Cristina R. ;
Liebler, Daniel C. .
JOURNAL OF PROTEOME RESEARCH, 2012, 11 (07) :3908-3913
[9]
Comprehensive molecular portraits of human breast tumours [J].
Koboldt, Daniel C. ;
Fulton, Robert S. ;
McLellan, Michael D. ;
Schmidt, Heather ;
Kalicki-Veizer, Joelle ;
McMichael, Joshua F. ;
Fulton, Lucinda L. ;
Dooling, David J. ;
Ding, Li ;
Mardis, Elaine R. ;
Wilson, Richard K. ;
Ally, Adrian ;
Balasundaram, Miruna ;
Butterfield, Yaron S. N. ;
Carlsen, Rebecca ;
Carter, Candace ;
Chu, Andy ;
Chuah, Eric ;
Chun, Hye-Jung E. ;
Coope, Robin J. N. ;
Dhalla, Noreen ;
Guin, Ranabir ;
Hirst, Carrie ;
Hirst, Martin ;
Holt, Robert A. ;
Lee, Darlene ;
Li, Haiyan I. ;
Mayo, Michael ;
Moore, Richard A. ;
Mungall, Andrew J. ;
Pleasance, Erin ;
Robertson, A. Gordon ;
Schein, Jacqueline E. ;
Shafiei, Arash ;
Sipahimalani, Payal ;
Slobodan, Jared R. ;
Stoll, Dominik ;
Tam, Angela ;
Thiessen, Nina ;
Varhol, Richard J. ;
Wye, Natasja ;
Zeng, Thomas ;
Zhao, Yongjun ;
Birol, Inanc ;
Jones, Steven J. M. ;
Marra, Marco A. ;
Cherniack, Andrew D. ;
Saksena, Gordon ;
Onofrio, Robert C. ;
Pho, Nam H. .
NATURE, 2012, 490 (7418) :61-70
[10]
A model for random sampling and estimation of relative protein abundance in shotgun proteomics [J].
Liu, HB ;
Sadygov, RG ;
Yates, JR .
ANALYTICAL CHEMISTRY, 2004, 76 (14) :4193-4201