The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
Shi, Leming; Campbell, Gregory; Jones, Wendell D.; Campagne, Fabien; Wen, Zhining; Walker, Stephen J.; Su, Zhenqiang; Chu, Tzu-Ming; Goodsaid, Federico M.; Pusztai, Lajos; Shaughnessy, John D.; Oberthuer, Andre; Thomas, Russell S.; Paules, Richard S.; Fielden, Mark; Barlogie, Bart; Chen, Weijie; Du, Pan; Fischer, Matthias; Furlanello, Cesare; Gallas, Brandon D.; Ge, Xijin; Megherbi, Dalila B.; Symmans, W. Fraser; Wang, May D.; Zhang, John; Bitter, Hans; Brors, Benedikt; Bushel, Pierre R.; Bylesjo, Max; Chen, Minjun; Cheng, Jie; Cheng, Jing; Chou, Jeff; Davison, Timothy S.; Delorenzi, Mauro; Deng, Youping; Devanarayan, Viswanath; Dix, David J.; Dopazo, Joaquin; Dorff, Kevin C.; Elloumi, Fathi; Fan, Jianqing; Fan, Shicai; Fan, Xiaohui; Fang, Hong; Gonzaludo, Nina; Hess, Kenneth R.; Hong, Huixiao; Huan, Jun; Irizarry, Rafael A.; Judson, Richard; Juraeva, Dilafruz; Lababidi, Samir; Lambert, Christophe G.; Li, Li; Li, Yanen; Li, Zhen; Lin, Simon M.; Liu, Guozhen; Lobenhofer, Edward K.; Luo, Jun; Luo, Wen; McCall, Matthew N.; Nikolsky, Yuri; Pennello, Gene A.; Perkins, Roger G.; Philip, Reena; Popovici, Vlad; Price, Nathan D.; Qian, Feng; Scherer, Andreas; Shi, Tieliu; Shi, Weiwei; Sung, Jaeyun; Thierry-Mieg, Danielle; Thierry-Mieg, Jean; Thodima, Venkata; Trygg, Johan; Vishnuvajjala, Lakshmi; Wang, Sue Jane; Wu, Jianping; Wu, Yichao; Xie, Qian; Yousef, Waleed A.; Zhang, Liang; Zhang, Xuegong; Zhong, Sheng; Zhou, Yiming; Zhu, Sheng; Arasappan, Dhivya; Bao, Wenjun; Lucas, Anne Bergstrom; Berthold, Frank; Brennan, Richard J.; Buness, Andreas; Catalano, Jennifer G.; Chang, Chang; Chen, Rong; Cheng, Yiyu; Cui, Jian; Czika, Wendy; Demichelis, Francesca; Deng, Xutao; Dosymbekov, Damir; Eils, Roland; Feng, Yang; Fostel, Jennifer; Fulmer-Smentek, Stephanie; Fuscoe, James C.; Gatto, Laurent; Ge, Weigong; Goldstein, Darlene R.; Guo, Li; Halbert, Donald N.; Han, Jing; Harris, Stephen C.; Hatzis, Christos; Herman, Damir; Huang, Jianping; Jensen, Roderick V.; Jiang, Rui; Johnson, Charles D.; Jurman, Giuseppe; Kahlert, Yvonne; Khuder, Sadik A.; Kohl, Matthias; Li, Jianying; Li, Li; Li, Menglong; Li, Quan-Zhen; Li, Shao; Li, Zhiguang; Liu, Jie; Liu, Ying; Liu, Zhichao; Meng, Lu; Madera, Manuel; Martinez-Murillo, Francisco; Medina, Ignacio; Meehan, Joseph; Miclaus, Kelci; Moffitt, Richard A.; Montaner, David; Mukherjee, Piali; Mulligan, George J.; Neville, Padraic; Nikolskaya, Tatiana; Ning, Baitang; Page, Grier P.; Parker, Joel; Parry, R. Mitchell; Peng, Xuejun; Peterson, Ron L.; Phan, John H.; Quanz, Brian; Ren, Yi; Riccadonna, Samantha; Roter, Alan H.; Samuelson, Frank W.; Schumacher, Martin M.; Shambaugh, Joseph D.; Shi, Qiang; Shippy, Richard; Si, Shengzhu; Smalter, Aaron; Sotiriou, Christos; Soukup, Mat; Staedtler, Frank; Steiner, Guido; Stokes, Todd H.; Sun, Qinglan; Tan, Pei-Yi; Tang, Rong; Tezak, Zivana; Thorn, Brett; Tsyganova, Marina; Turpaz, Yaron; Vega, Silvia C.; Visintainer, Roberto; von Frese, Juergen; Wang, Charles; Wang, Eric; Wang, Junwei; Wang, Wei; Westermann, Frank; Willey, James C.; Woods, Matthew; Wu, Shujian; Xiao, Nianqing; Xu, Joshua; Xu, Lei; Yang, Lun; Zeng, Xiao; Zhang, Jialu; Zhang, Li; Zhang, Min; Zhao, Chen; Puri, Raj K.; Scherf, Uwe; Tong, Weida; Wolfinger, Russell D.
2010
Abstract
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.
Details
Title
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
Author(s)
Shi, Leming ; Campbell, Gregory ; Jones, Wendell D. ; Campagne, Fabien ; Wen, Zhining ; Walker, Stephen J. ; Su, Zhenqiang ; Chu, Tzu-Ming ; Goodsaid, Federico M. ; Pusztai, Lajos ; Shaughnessy, John D. ; Oberthuer, Andre ; Thomas, Russell S. ; Paules, Richard S. ; Fielden, Mark ; Barlogie, Bart ; Chen, Weijie ; Du, Pan ; Fischer, Matthias ; Furlanello, Cesare ; Gallas, Brandon D. ; Ge, Xijin ; Megherbi, Dalila B. ; Symmans, W. Fraser ; Wang, May D. ; Zhang, John ; Bitter, Hans ; Brors, Benedikt ; Bushel, Pierre R. ; Bylesjo, Max ; Chen, Minjun ; Cheng, Jie ; Cheng, Jing ; Chou, Jeff ; Davison, Timothy S. ; Delorenzi, Mauro ; Deng, Youping ; Devanarayan, Viswanath ; Dix, David J. ; Dopazo, Joaquin ; Dorff, Kevin C. ; Elloumi, Fathi ; Fan, Jianqing ; Fan, Shicai ; Fan, Xiaohui ; Fang, Hong ; Gonzaludo, Nina ; Hess, Kenneth R. ; Hong, Huixiao ; Huan, Jun ; Irizarry, Rafael A. ; Judson, Richard ; Juraeva, Dilafruz ; Lababidi, Samir ; Lambert, Christophe G. ; Li, Li ; Li, Yanen ; Li, Zhen ; Lin, Simon M. ; Liu, Guozhen ; Lobenhofer, Edward K. ; Luo, Jun ; Luo, Wen ; McCall, Matthew N. ; Nikolsky, Yuri ; Pennello, Gene A. ; Perkins, Roger G. ; Philip, Reena ; Popovici, Vlad ; Price, Nathan D. ; Qian, Feng ; Scherer, Andreas ; Shi, Tieliu ; Shi, Weiwei ; Sung, Jaeyun ; Thierry-Mieg, Danielle ; Thierry-Mieg, Jean ; Thodima, Venkata ; Trygg, Johan ; Vishnuvajjala, Lakshmi ; Wang, Sue Jane ; Wu, Jianping ; Wu, Yichao ; Xie, Qian ; Yousef, Waleed A. ; Zhang, Liang ; Zhang, Xuegong ; Zhong, Sheng ; Zhou, Yiming ; Zhu, Sheng ; Arasappan, Dhivya ; Bao, Wenjun ; Lucas, Anne Bergstrom ; Berthold, Frank ; Brennan, Richard J. ; Buness, Andreas ; Catalano, Jennifer G. ; Chang, Chang ; Chen, Rong ; Cheng, Yiyu ; Cui, Jian ; Czika, Wendy ; Demichelis, Francesca ; Deng, Xutao ; Dosymbekov, Damir ; Eils, Roland ; Feng, Yang ; Fostel, Jennifer ; Fulmer-Smentek, Stephanie ; Fuscoe, James C. ; Gatto, Laurent ; Ge, Weigong ; Goldstein, Darlene R. ; Guo, Li ; Halbert, Donald N. ; Han, Jing ; Harris, Stephen C. ; Hatzis, Christos ; Herman, Damir ; Huang, Jianping ; Jensen, Roderick V. ; Jiang, Rui ; Johnson, Charles D. ; Jurman, Giuseppe ; Kahlert, Yvonne ; Khuder, Sadik A. ; Kohl, Matthias ; Li, Jianying ; Li, Li ; Li, Menglong ; Li, Quan-Zhen ; Li, Shao ; Li, Zhiguang ; Liu, Jie ; Liu, Ying ; Liu, Zhichao ; Meng, Lu ; Madera, Manuel ; Martinez-Murillo, Francisco ; Medina, Ignacio ; Meehan, Joseph ; Miclaus, Kelci ; Moffitt, Richard A. ; Montaner, David ; Mukherjee, Piali ; Mulligan, George J. ; Neville, Padraic ; Nikolskaya, Tatiana ; Ning, Baitang ; Page, Grier P. ; Parker, Joel ; Parry, R. Mitchell ; Peng, Xuejun ; Peterson, Ron L. ; Phan, John H. ; Quanz, Brian ; Ren, Yi ; Riccadonna, Samantha ; Roter, Alan H. ; Samuelson, Frank W. ; Schumacher, Martin M. ; Shambaugh, Joseph D. ; Shi, Qiang ; Shippy, Richard ; Si, Shengzhu ; Smalter, Aaron ; Sotiriou, Christos ; Soukup, Mat ; Staedtler, Frank ; Steiner, Guido ; Stokes, Todd H. ; Sun, Qinglan ; Tan, Pei-Yi ; Tang, Rong ; Tezak, Zivana ; Thorn, Brett ; Tsyganova, Marina ; Turpaz, Yaron ; Vega, Silvia C. ; Visintainer, Roberto ; von Frese, Juergen ; Wang, Charles ; Wang, Eric ; Wang, Junwei ; Wang, Wei ; Westermann, Frank ; Willey, James C. ; Woods, Matthew ; Wu, Shujian ; Xiao, Nianqing ; Xu, Joshua ; Xu, Lei ; Yang, Lun ; Zeng, Xiao ; Zhang, Jialu ; Zhang, Li ; Zhang, Min ; Zhao, Chen ; Puri, Raj K. ; Scherf, Uwe ; Tong, Weida ; Wolfinger, Russell D.
Published in
Nature Biotechnology
Volume
28
Pages
827-U109
Date
2010
Publisher
Nature Publishing Group
ISSN
1087-0156
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Laboratories
STAT
Record Appears in
Scientific production and competences > SB - School of Basic Sciences > MATH - Institute of Mathematics > STAT - Chair of Statistics
Scientific production and competences > SB - School of Basic Sciences > Mathematics
Peer-reviewed publications
Work produced at EPFL
Journal Articles
Published
Scientific production and competences > SB - School of Basic Sciences > Mathematics
Peer-reviewed publications
Work produced at EPFL
Journal Articles
Published
Record creation date
2011-12-16