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The MicroArray Quality Control (MAQC)-IIII study of common practices for the development and validation of microarray-based predictive models
Shi, Leming1; Campbell, Gregory2; Jones, Wendell D.3; Campagne, Fabien4; Wen, Zhining1; Walker, Stephen J.5; Su, Zhenqiang6; Chu, Tzu-Ming7; Goodsaid, Federico M.8; Pusztai, Lajos9; Shaughnessy, John D., Jr.10; Oberthuer, Andre11,12; Thomas, Russell S.13; Paules, Richard S.14; Fielden, Mark15; Barlogie, Bart10; Chen, Weijie2; Du, Pan16; Fischer, Matthias11,12; Furlanello, Cesare17; Gallas, Brandon D.2; Ge, Xijin18; Megherbi, Dalila B.19; Symmans, W. Fraser20; Wang, May D.21,22; Zhang, John23; Bitter, Hans24; Brors, Benedikt25; Bushel, Pierre R.14; Bylesjo, Max26; Chen, Minjun1; Cheng, Jie27; Cheng, Jing28; Chou, Jeff14; Davison, Timothy S.29; Delorenzi, Mauro30; Deng, Youping31; Devanarayan, Viswanath32; Dix, David J.33; Dopazo, Joaquin34; Dorff, Kevin C.; Elloumi, Fathi33; Fan, Jianqing35; Fan, Shicai36; Fan, Xiaohui37; Fang, Hong6; Gonzaludo, Nina38; Hess, Kenneth R.39; Hong, Huixiao1; Huan, Jun40; Irizarry, Rafael A.41; Judson, Richard33; Juraeva, Dilafruz25; Lababidi, Samir42; Lambert, Christophe G.43; Li, Li7; Li, Yanen44; Li, Zhen33; Lin, Simon M.16; Liu, Guozhen45; Lobenhofer, Edward K.46; Luo, Jun23; Luo, Wen47; McCall, Matthew N.41; Nikolsky, Yuri48; Pennello, Gene A.2; Perkins, Roger G.1; Philip, Reena2; Popovici, Vlad30; Price, Nathan D.49; Qian, Feng6; Scherer, Andreas50; Shi, Tieliu51,52; Shi, Weiwei48; Sung, Jaeyun49; Thierry-Mieg, Danielle53; Thierry-Mieg, Jean53; Thodima, Venkata54; Trygg, Johan26; Vishnuvajjala, Lakshmi2; Wang, Sue Jane8; Wu, Jianping55; Wu, Yichao56; Xie, Qian57; Yousef, Waleed A.58; Zhang, Liang55; Zhang, Xuegong36; Zhong, Sheng59; Zhou, Yiming10; Zhu, Sheng55; Arasappan, Dhivya6; Bao, Wenjun7; Lucas, Anne Bergstrom60; Berthold, Frank11,12; Brennan, Richard J.48; Buness, Andreas61; Catalano, Jennifer G.42; Chang, Chang51,52; Chen, Rong62; Cheng, Yiyu37; Cui, Jian51,52; Czika, Wendy7; Demichelis, Francesca63,64; Deng, Xutao65; Dosymbekov, Damir66; Eils, Roland25; Feng, Yang35; Fostel, Jennifer14; Fulmer-Smentek, Stephanie60; Fuscoe, James C.1; Gatto, Laurent67; Ge, Weigong1; Goldstein, Darlene R.68; Guo, Li69; Halbert, Donald N.70; Han, Jing42; Harris, Stephen C.1; Hatzis, Christos71; Herman, Damir72; Huang, Jianping37; Jensen, Roderick V.73; Jiang, Rui36; Johnson, Charles D.74; Jurman, Giuseppe17; Kahlert, Yvonne11,12; Khuder, Sadik A.75; Kohl, Matthias76; Li, Jianying77; Li, Li78; Li, Menglong79; Li, Quan-Zhen80; Li, Shao37; Li, Zhiguang1; Liu, Jie1; Liu, Ying36; Liu, Zhichao1; Meng, Lu36; Madera, Manuel19; Martinez-Murillo, Francisco2; Medina, Ignacio81; Meehan, Joseph6; Miclaus, Kelci7; Moffitt, Richard A.21,22; Montaner, David81; Mukherjee, Piali; Mulligan, George J.82; Neville, Padraic7; Nikolskaya, Tatiana48; Ning, Baitang1; Page, Grier P.83; Parker, Joel3; Parry, R. Mitchell21,22; Peng, Xuejun84; Peterson, Ron L.85; Phan, John H.21,22; Quanz, Brian40; Ren, Yi86; Riccadonna, Samantha17; Roter, Alan H.87; Samuelson, Frank W.2; Schumacher, Martin M.88; Shambaugh, Joseph D.89; Shi, Qiang1; Shippy, Richard90; Si, Shengzhu91; Smalter, Aaron40; Sotiriou, Christos92; Soukup, Mat8; Staedtler, Frank88; Steiner, Guido93; Stokes, Todd H.21,22; Sun, Qinglan55; Tan, Pei-Yi7; Tang, Rong2; Tezak, Zivana2; Thorn, Brett1; Tsyganova, Marina66; Turpaz, Yaron94; Vega, Silvia C.95; Visintainer, Roberto17; von Frese, Juergen96; Wang, Charles65; Wang, Eric23; Wang, Junwei51,52; Wang, Wei97; Westermann, Frank25; Willey, James C.98; Woods, Matthew23; Wu, Shujian99; Xiao, Nianqing100; Xu, Joshua6; Xu, Lei1; Yang, Lun1; Zeng, Xiao45; Zhang, Jialu8; Zhang, Li8; Zhang, Min1; Zhao, Chen51,52; Puri, Raj K.42; Scherf, Uwe2; Tong, Weida1; Wolfinger, Russell D.7; MAQC Consortium; Shi, LM
2010-08-01
发表期刊NATURE BIOTECHNOLOGY
ISSN1087-0156
卷号28期号:8页码:827-U109
摘要Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.
关键词Gene-expression Data Control Maqc Project Multiple-myeloma Breast-cancer Published Microarray Follicular Lymphoma Risk-stratification Dna Microarrays Classification Performance
文章类型Article
WOS标题词Science & Technology ; Life Sciences & Biomedicine
DOI10.1038/nbt.1665
收录类别SCI
语种英语
关键词[WOS]GENE-EXPRESSION DATA ; CONTROL MAQC PROJECT ; MULTIPLE-MYELOMA ; BREAST-CANCER ; PUBLISHED MICROARRAY ; FOLLICULAR LYMPHOMA ; RISK-STRATIFICATION ; DNA MICROARRAYS ; CLASSIFICATION ; PERFORMANCE
WOS研究方向Biotechnology & Applied Microbiology
WOS类目Biotechnology & Applied Microbiology
WOS记录号WOS:000280757500023
引用统计
被引频次:387[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
版本出版稿
条目标识符http://ir.ipe.ac.cn/handle/122111/6111
专题多相复杂系统国家重点实验室
通讯作者Shi, LM
作者单位1.US FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA
2.US FDA, Ctr Devices & Radiol Hlth, Silver Spring, MD USA
3.Express Anal Inc, Durham, NC USA
4.Cornell Univ, Dept Physiol & Biophys, Weill Med Coll, New York, NY 10021 USA
5.Wake Forest Univ, Wake Forest Inst Regenerat Med, Winston Salem, NC 27109 USA
6.Z Tech, Jefferson, AR USA
7.SAS Inst Inc, Cary, NC USA
8.US FDA, Ctr Drug Evaluat & Res, Silver Spring, MD USA
9.Univ Texas MD Anderson Canc Ctr, Breast Med Oncol Dept, Houston, TX 77030 USA
10.Univ Arkansas Med Sci, Myeloma Inst Res & Therapy, Little Rock, AR 72205 USA
11.Univ Cologne, Dept Pediat Oncol & Hematol, Cologne, Germany
12.Univ Cologne, Ctr Mol Med CMMC, Cologne, Germany
13.Hamner Inst Hlth Sci, Res Triangle Pk, NC USA
14.Natl Inst Environm Hlth Sci, NIH, Res Triangle Pk, NC USA
15.Roche Palo Alto LLC, San Francisco, CA USA
16.Northwestern Univ, Biomed Informat Ctr, Chicago, IL 60611 USA
17.Fdn Bruno Kessler, Povo, Italy
18.S Dakota State Univ, Dept Math & Stat, Brookings, SD 57007 USA
19.Univ Massachusetts Lowell, CMINDS Res Ctr, Dept Elect & Comp Engn, Lowell, MA USA
20.UI MD Anderson Canc Ctr, Dept Pathol, Houston, TX USA
21.Georgia Inst Technol, Dept Biomed Engn, Atlanta, GA 30332 USA
22.Emory Univ, Atlanta, GA 30322 USA
23.Syst Analyt Inc, Waltham, MA USA
24.Hoffmann LaRoche, Nutley, NJ USA
25.German Canc Res Ctr, Dept Theoret Bioinformat, Heidelberg, Germany
26.Umea Univ, Computat Life Sci Cluster CLiC, Chem Biol Ctr KBC, Umea, Sweden
27.GlaxoSmithKline Inc, Collegeville, PA USA
28.Tsinghua Univ, Sch Med, Med Syst Biol Res Ctr, Beijing 100084, Peoples R China
29.Almac Diagnost Ltd, Craigavon, North Ireland
30.Swiss Inst Bioinformat, Lausanne, Switzerland
31.Univ So Mississippi, Dept Biol Sci, Hattiesburg, MS 39406 USA
32.Global Pharmaceut R&D, Abbott Labs, Souderton, PA USA
33.US EPA, Natl Ctr Computat Toxicol, Res Triangle Pk, NC 27711 USA
34.CIPF, Dept Bioinformat & Genom, Valencia, Spain
35.Princeton Univ, Dept Operat Res & Financial Engn, Princeton, NJ 08544 USA
36.Tsinghua Univ, MOE Key Lab Bioinformat, TNLIST, Dept Automat, Beijing 100084, Peoples R China
37.Zhejiang Univ, Coll Pharmaceut Sci, Inst Pharmaceut Informat, Hangzhou 310003, Zhejiang, Peoples R China
38.Roche Palo Alto LLC, Palo Alto, CA USA
39.UT MD Anderson Canc Ctr, Dept Biostat, Houston, TX USA
40.Univ Kansas, Dept Elect Engn & Comp Sci, Lawrence, KS 66045 USA
41.Johns Hopkins Univ, Dept Biostat, Baltimore, MD 21205 USA
42.US FDA, Ctr Biol Evaluat & Res, Bethesda, MD USA
43.Golden Helix Inc, Bozeman, MT USA
44.Univ Illinois, Dept Comp Sci, Urbana, IL 61801 USA
45.SABiosciences Corp, Frederick, MD USA
46.Cogenics, Morrisville, NC USA
47.Ligand Pharmaceut Inc, La Jolla, CA 92037 USA
48.GeneGo Inc, Encinitas, CA USA
49.Univ Illinois, Dept Chem & Biomol Engn, Urbana, IL 61801 USA
50.Spheromics, Kontiolahti, Finland
51.E China Normal Univ, Ctr Bioinformat, Shanghai 200062, Peoples R China
52.E China Normal Univ, Inst Biomed Sci, Sch Life Sci, Shanghai 200062, Peoples R China
53.Natl Ctr Biotechnol Informat, NIH, Bethesda, MD USA
54.Mem Sloan Kettering Canc Ctr, Rockefeller Res Labs, New York, NY 10021 USA
55.CapitalBio Corp, Beijing, Peoples R China
56.N Carolina State Univ, Dept Stat, Raleigh, NC 27695 USA
57.SRA Int FMMFS, Rockville, MD USA
58.Helwan Univ, Helwan, Egypt
59.Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA
60.Agilent Technol, Santa Clara, CA USA
61.F Hoffmann La Roche Ltd, Basel, Switzerland
62.Stanford Univ, Stanford Ctr Biomed Informat Res, Stanford, CA 94305 USA
63.Cornell Univ, Weill Med Coll, Dept Pathol, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA
64.Cornell Univ, Weill Med Coll, Lab Med, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA
65.Univ Calif Los Angeles, Cedars Sinai Med Ctr, David Geffen Sch Med, Los Angeles, CA 90048 USA
66.Russian Acad Sci, Vavilov Inst Gen Genet, Moscow, Russia
67.DNAVision SA, Gosselies, Belgium
68.Ecole Polytech Fed Lausanne, Lausanne, Switzerland
69.Chinese Acad Sci, Inst Proc Engn, State Key Lab Multiphase Complex Syst, Beijing, Peoples R China
70.Abbott Labs, Abbott Pk, IL 60064 USA
71.Nuvera Biosci Inc, Woburn, MA USA
72.Univ Arkansas Med Sci, Winthrop P Rockefeller Canc Inst, Little Rock, AR 72205 USA
73.VirginiaTech, Blacksburg, VA USA
74.BioMath Solut LLC, Austin, TX USA
75.Univ Toledo, Bioinformat Program, Toledo, OH 43606 USA
76.Univ Bayreuth, Dept Math, Bayreuth, Germany
77.Univ N Carolina, Lineberger Comprehens Canc Ctr, Chapel Hill, NC 27599 USA
78.Stanford Univ, Dept Pediat, Stanford, CA 94305 USA
79.Sichuan Univ, Coll Chem, Chengdu 610064, Sichuan, Peoples R China
80.Univ Texas SW Med Ctr Dallas, Dallas, TX 75390 USA
81.CIPF, Valencia, Spain
82.Millennium Pharmaceut Inc, Cambridge, MA USA
83.RTI Int, Atlanta, GA USA
84.Takeda Global R&D Ctr Inc, Deerfield, IL USA
85.Novartis Inst Biomed Res, Cambridge, MA USA
86.Rutgers State Univ, WM Keck Ctr Collaborat Neurosci, Piscataway, NJ USA
87.Entelos Inc, Foster City, CA USA
88.Novartis Pharma AG, Biomarker Dev, Novartis Inst BioMed Res, Basel, Switzerland
89.Genedata Inc, Lexington, MA USA
90.Affymetrix Inc, Santa Clara, CA USA
91.Hefei Teachers Coll, Dept Chem & Chem Engn, Hefei, Anhui, Peoples R China
92.Inst Jules Bordet, B-1000 Brussels, Belgium
93.F Hoffmann La Roche Ltd, Biostat, Basel, Switzerland
94.Lilly Singapore, Ctr Drug Discovery, Immunos, Singapore, Singapore
95.Microsoft Corp, US Hlth Solut Grp, Redmond, WA 98052 USA
96.Data Anal Solut DA SOL GmbH, Greifenberg, Germany
97.Cornell Univ, Ithaca, NY USA
98.Univ Toledo Hlth Sci Campus, Dept Med, Div Pulm & Crit Care Med, Toledo, OH USA
99.Bristol Myers Squibb, Pennington, NJ USA
100.OpGen Inc, Gaithersburg, MD USA
101.Tsinghua Univ, TNLIST, Dept Automat, Bioinformat Div, Beijing 100084, Peoples R China
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Shi, Leming,Campbell, Gregory,Jones, Wendell D.,et al. The MicroArray Quality Control (MAQC)-IIII study of common practices for the development and validation of microarray-based predictive models[J]. NATURE BIOTECHNOLOGY,2010,28(8):827-U109.
APA Shi, Leming.,Campbell, Gregory.,Jones, Wendell D..,Campagne, Fabien.,Wen, Zhining.,...&Shi, LM.(2010).The MicroArray Quality Control (MAQC)-IIII study of common practices for the development and validation of microarray-based predictive models.NATURE BIOTECHNOLOGY,28(8),827-U109.
MLA Shi, Leming,et al."The MicroArray Quality Control (MAQC)-IIII study of common practices for the development and validation of microarray-based predictive models".NATURE BIOTECHNOLOGY 28.8(2010):827-U109.
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