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The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

  1. Author:
    Shi, L. M.
    Campbell, G.
    Jones, W. D.
    Campagne, F.
    Wen, Z. N.
    Walker, S. J.
    Su, Z. Q.
    Chu, T. M.
    Goodsaid, F. M.
    Pusztai, L.
    Shaughnessy, J. D.
    Oberthuer, A.
    Thomas, R. S.
    Paules, R. S.
    Fielden, M.
    Barlogie, B.
    Chen, W. J.
    Du, P.
    Fischer, M.
    Furlanello, C.
    Gallas, B. D.
    Ge, X. J.
    Megherbi, D. B.
    Symmans, W. F.
    Wang, M. D.
    Zhang, J.
    Bitter, H.
    Brors, B.
    Bushel, P. R.
    Bylesjo, M.
    Chen, M. J.
    Cheng, J.
    Chou, J.
    Davison, T. S.
    Delorenzi, M.
    Deng, Y. P.
    Devanarayan, V.
    Dix, D. J.
    Dopazo, J.
    Dorff, K. C.
    Elloumi, F.
    Fan, J. Q.
    Fan, S. C.
    Fan, X. H.
    Fang, H.
    Gonzaludo, N.
    Hess, K. R.
    Hong, H. X.
    Huan, J.
    Irizarry, R. A.
    Judson, R.
    Juraeva, D.
    Lababidi, S.
    Lambert, C. G.
    Li, L.
    Li, Y. N.
    Li, Z.
    Lin, S. M.
    Liu, G. Z.
    Lobenhofer, E. K.
    Luo, J.
    Luo, W.
    McCall, M. N.
    Nikolsky, Y.
    Pennello, G. A.
    Perkins, R. G.
    Philip, R.
    Popovici, V.
    Price, N. D.
    Qian, F.
    Scherer, A.
    Shi, T. L.
    Shi, W. W.
    Sung, J.
    Thierry-Mieg, D.
    Thierry-Mieg, J.
    Thodima, V.
    Trygg, J.
    Vishnuvajjala, L.
    Wang, S. J.
    Wu, J. P.
    Wu, Y. C.
    Xie, Q. A.
    Yousef, W. A.
    Zhang, L. A.
    Zhang, X. G.
    Zhong, S.
    Zhou, Y. M.
    Zhu, S.
    Arasappan, D.
    Bao, W. J.
    Lucas, A. B.
    Berthold, F.
    Brennan, R. J.
    Buness, A.
    Catalano, J. G.
    Chang, C.
    Chen, R.
    Cheng, Y. Y.
    Cui, J. A.
    Czika, W.
    Demichelis, F.
    Deng, X. T.
    Dosymbekov, D.
    Eils, R.
    Feng, Y.
    Fostel, J.
    Fulmer-Smentek, S.
    Fuscoe, J. C.
    Gatto, L.
    Ge, W. G.
    Goldstein, D. R.
    Guo, L.
    Halbert, D. N.
    Han, J.
    Harris, S. C.
    Hatzis, C.
    Herman, D.
    Huang, J. P.
    Jensen, R. V.
    Jiang, R.
    Johnson, C. D.
    Jurman, G.
    Kahlert, Y.
    Khuder, S. A.
    Kohl, M.
    Li, J. Y.
    Li, M. L.
    Li, Q. Z.
    Li, S.
    Li, Z. G.
    Liu, J.
    Liu, Y.
    Liu, Z. C.
    Meng, L.
    Madera, M.
    Martinez-Murillo, F.
    Medina, I.
    Meehan, J.
    Miclaus, K.
    Moffitt, R. A.
    Montaner, D.
    Mukherjee, P.
    Mulligan, G. J.
    Neville, P.
    Nikolskaya, T.
    Ning, B. T.
    Page, G. P.
    Parker, J.
    Parry, R. M.
    Peng, X. J.
    Peterson, R. L.
    Phan, J. H.
    Quanz, B.
    Ren, Y.
    Riccadonna, S.
    Roter, A. H.
    Samuelson, F. W.
    Schumacher, M. M.
    Shambaugh, J. D.
    Shi, Q. A.
    Shippy, R.
    Si, S. Z.
    Smalter, A.
    Sotiriou, C.
    Soukup, M.
    Staedtler, F.
    Steiner, G.
    Stokes, T. H.
    Sun, Q. L.
    Tan, P. Y.
    Tang, R.
    Tezak, Z.
    Thorn, B.
    Tsyganova, M.
    Turpaz, Y.
    Vega, S. C.
    Visintainer, R.
    von Frese, J.
    Wang, C.
    Wang, E.
    Wang, J. W.
    Wang, W.
    Westermann, F.
    Willey, J. C.
    Woods, M.
    Wu, S. J.
    Xiao, N. Q.
    Xu, J.
    Xu, L.
    Yang, L.
    Zeng, X. A.
    Zhang, J. L.
    Zhang, L.
    Zhang, M.
    Zhao, C.
    Puri, R. K.
    Scherf, U.
    Tong, W. D.
    Wolfinger, R. D.
    Consortium, M.

  2. Author Address

    [Shi, Leming; Wen, Zhining; Chen, Minjun; Hong, Huixiao; Perkins, Roger G.; Fuscoe, James C.; Ge, Weigong; Harris, Stephen C.; Li, Zhiguang; Liu, Jie; Liu, Zhichao; Ning, Baitang; Shi, Qiang; Thorn, Brett; Xu, Lei; Yang, Lun; Zhang, Min; Tong, Weida] US FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA. [Campbell, Gregory; Chen, Weijie; Gallas, Brandon D.; Pennello, Gene A.; Philip, Reena; Vishnuvajjala, Lakshmi; Martinez-Murillo, Francisco; Samuelson, Frank W.; Tang, Rong; Tezak, Zivana; Scherf, Uwe] US FDA, Ctr Devices & Radiol Hlth, Silver Spring, MD USA. [Jones, Wendell D.; Parker, Joel] Express Anal Inc, Durham, NC USA. [Campagne, Fabien] Cornell Univ, Dept Physiol & Biophys, Weill Med Coll, New York, NY 10021 USA. [Campagne, Fabien; Dorff, Kevin C.; Demichelis, Francesca; Mukherjee, Piali] Cornell Univ, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, Weill Med Coll, New York, NY 10021 USA. [Walker, Stephen J.] Wake Forest Univ, Wake Forest Inst Regenerat Med, Winston Salem, NC 27109 USA. [Su, Zhenqiang; Fang, Hong; Qian, Feng; Arasappan, Dhivya; Meehan, Joseph; Xu, Joshua] NCTR FDA, Z Tech, Jefferson, AR USA. [Chu, Tzu-Ming; Li, Li; Bao, Wenjun; Czika, Wendy; Miclaus, Kelci; Neville, Padraic; Tan, Pei-Yi; Wolfinger, Russell D.] SAS Inst Inc, Cary, NC USA. [Goodsaid, Federico M.; Wang, Sue Jane; Soukup, Mat; Zhang, Jialu; Zhang, Li] US FDA, Ctr Drug Evaluat & Res, Silver Spring, MD USA. [Pusztai, Lajos] Univ Texas MD Anderson Canc Ctr, Breast Med Oncol Dept, Houston, TX 77030 USA. [Shaughnessy, John D., Jr.; Barlogie, Bart; Zhou, Yiming] Univ Arkansas Med Sci, Myeloma Inst Res & Therapy, Little Rock, AR 72205 USA. [Oberthuer, Andre; Fischer, Matthias; Berthold, Frank; Kahlert, Yvonne] Univ Cologne, Dept Pediat Oncol & Hematol, Cologne, Germany. [Oberthuer, Andre; Fischer, Matthias; Berthold, Frank; Kahlert, Yvonne] Univ Cologne, Ctr Mol Med CMMC, Cologne, Germany. [Thomas, Russell S.] Hamner Inst Hlth Sci, Res Triangle Pk, NC USA. [Paules, Richard S.; Bushel, Pierre R.; Chou, Jeff; Fostel, Jennifer] NIEHS, NIH, Res Triangle Pk, NC 27709 USA. [Fielden, Mark] Roche Palo Alto LLC, San Francisco, CA USA. [Du, Pan; Lin, Simon M.] Northwestern Univ, Biomed Informat Ctr, Chicago, IL 60611 USA. [Furlanello, Cesare; Jurman, Giuseppe; Riccadonna, Samantha; Visintainer, Roberto] Fdn Bruno Kessler, Povo, Trento, Italy. [Ge, Xijin] S Dakota State Univ, Dept Math & Stat, Brookings, SD 57007 USA. [Megherbi, Dalila B.; Madera, Manuel] Univ Massachusetts, CMINDS Res Ctr, Dept Elect & Comp Engn, Lowell, MA USA. [Symmans, W. Fraser] Univ Texas MD Anderson Canc Ctr, Dept Pathol, Houston, TX 77030 USA. [Wang, May D.; Moffitt, Richard A.; Parry, R. Mitchell; Phan, John H.; Stokes, Todd H.] Georgia Inst Technol, Dept Biomed Engn, Atlanta, GA 30332 USA. [Wang, May D.; Moffitt, Richard A.; Parry, R. Mitchell; Phan, John H.; Stokes, Todd H.] Emory Univ, Atlanta, GA 30322 USA. [Zhang, John; Luo, Jun; Wang, Eric; Woods, Matthew] Syst Analyt Inc, Waltham, MA USA. [Bitter, Hans] Hoffmann La Roche Inc, Nutley, NJ 07110 USA. [Brors, Benedikt; Juraeva, Dilafruz; Eils, Roland; Westermann, Frank] German Canc Res Ctr, Dept Theoret Bioinformat, Heidelberg, Germany. [Bylesjo, Max; Trygg, Johan] Umea Univ, Chem Biol Ctr KBC, Umea, Sweden. [Cheng, Jie] GlaxoSmithKline Inc, Collegeville, PA USA. [Cheng, Jing] Tsinghua Univ, Sch Med, Med Syst Biol Res Ctr, Beijing 100084, Peoples R China. [Davison, Timothy S.] Almac Diagnost Ltd, Craigavon, North Ireland. [Delorenzi, Mauro; Popovici, Vlad] Swiss Inst Bioinformat, Lausanne, Switzerland. [Deng, Youping] Univ So Mississippi, Dept Biol Sci, Hattiesburg, MS 39406 USA. [Devanarayan, Viswanath] Abbott Labs, Global Pharmaceut R&D, Souderton, PA USA. [Elloumi, Fathi; Judson, Richard; Li, Zhen] US EPA, Natl Ctr Computat Toxicol, Res Triangle Pk, NC 27711 USA. [Dopazo, Joaquin] CIPF, Dept Bioinformat & Genom, Valencia, Spain. [Fan, Jianqing; Feng, Yang] Princeton Univ, Dept Operat Res & Financial Engn, Princeton, NJ 08544 USA. [Fan, Shicai; Zhang, Xuegong; Jiang, Rui; Liu, Ying; Meng, Lu] Tsinghua Univ, TNLIST Dept Automat, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China. [Fan, Shicai; Zhang, Xuegong; Jiang, Rui; Liu, Ying; Meng, Lu] Tsinghua Univ, TNLIST Dept Automat, Bioinformat Div, Beijing 100084, Peoples R China. [Fan, Xiaohui; Cheng, Yiyu; Huang, Jianping; Li, Shao] Zhejiang Univ, Coll Pharmaceut Sci, Inst Pharmaceut Informat, Hangzhou 310003, Zhejiang, Peoples R China. [Gonzaludo, Nina] Roche Palo Alto LLC, Palo Alto, CA USA. [Hess, Kenneth R.] Univ Texas MD Anderson Canc Ctr, Dept Biostat, Houston, TX 77030 USA. [Huan, Jun; Quanz, Brian; Smalter, Aaron] Univ Kansas, Dept Elect Engn & Comp Sci, Lawrence, KS 66045 USA. [Irizarry, Rafael A.; McCall, Matthew N.] Johns Hopkins Univ, Dept Biostat, Baltimore, MD 21205 USA. [Lababidi, Samir; Catalano, Jennifer G.; Han, Jing; Puri, Raj K.] US FDA, Ctr Biol Evaluat & Res, Bethesda, MD USA. [Lambert, Christophe G.] Golden Helix Inc, Bozeman, MT USA. [Li, Yanen] Univ Illinois, Dept Comp Sci, Urbana, IL 61801 USA. [Liu, Guozhen; Zeng, Xiao] SABiosciences Corp, Frederick, MD USA. [Lobenhofer, Edward K.] Cogenics, Morrisville, NC USA. [Luo, Wen] Ligand Pharmaceut Inc, La Jolla, CA 92037 USA. [Nikolsky, Yuri; Shi, Weiwei; Brennan, Richard J.; Nikolskaya, Tatiana] GeneGo Inc, Encinitas, CA USA. [Price, Nathan D.; Sung, Jaeyun] Univ Illinois, Dept Chem & Biomol Engn, Urbana, IL 61801 USA. [Scherer, Andreas] Spheromics, Kontiolahti, Finland. [Shi, Tieliu; Chang, Chang; Cui, Jian; Wang, Junwei; Zhao, Chen] E China Normal Univ, Sch Life Sci, Ctr Bioinformat, Shanghai 200062, Peoples R China. [Shi, Tieliu; Chang, Chang; Cui, Jian; Wang, Junwei; Zhao, Chen] E China Normal Univ, Sch Life Sci, Inst Biomed Sci, Shanghai 200062, Peoples R China. [Thierry-Mieg, Danielle; Thierry-Mieg, Jean] NIH, Natl Ctr Biotechnol Informat, Bethesda, MD 20892 USA. [Thodima, Venkata] Mem Sloan Kettering Canc Ctr, Rockefeller Res Labs, New York, NY 10021 USA. [Wu, Jianping; Zhang, Liang; Zhu, Sheng; Sun, Qinglan] CapitalBio Corp, Beijing, Peoples R China. [Wu, Yichao] N Carolina State Univ, Dept Stat, Raleigh, NC 27695 USA. [Xie, Qian] SRA Int EMMES, Rockville, MD USA. [Yousef, Waleed A.] Helwan Univ, Helwan, Egypt. [Zhong, Sheng] Univ Illinois, Dept Bioengn, Urbana, IL 61801 USA. [Lucas, Anne Bergstrom; Fulmer-Smentek, Stephanie] Agilent Technol, Santa Clara, CA USA. [Steiner, Guido] F Hoffmann La Roche & Co Ltd, Biostat, CH-4002 Basel, Switzerland. [Chen, Rong] Stanford Univ, Stanford Ctr Biomed Informat Res, Stanford, CA 94305 USA. [Demichelis, Francesca] Cornell Univ, Dept Pathol & Lab Med, Weill Med Coll, New York, NY 10021 USA. [Deng, Xutao; Wang, Charles] Univ Calif Los Angeles, David Geffen Sch Med, Cedars Sinai Med Ctr, Los Angeles, CA 90095 USA. [Dosymbekov, Damir; Tsyganova, Marina] Russian Acad Sci, Vavilov Inst Gen Genet, Moscow, Russia. [Gatto, Laurent] DNAVision SA, Gosselies, Belgium. [Goldstein, Darlene R.] Ecole Polytech Fed Lausanne, CH-1015 Lausanne, Switzerland. [Guo, Li] Chinese Acad Sci, Inst Proc Engn, State Key Lab Multi Phase Complex Syst, Beijing, Peoples R China. [Halbert, Donald N.] Abbott Labs, Abbott Pk, IL 60064 USA. [Hatzis, Christos] Nuvera Biosci Inc, Woburn, MA USA. [Herman, Damir] Univ Arkansas Med Sci, Winthrop P Rockefeller Canc Inst, Little Rock, AR 72205 USA. [Jensen, Roderick V.] VirginiaTech, Blacksburg, VA USA. [Johnson, Charles D.] BioMath Solut LLC, Austin, TX USA. [Khuder, Sadik A.] Univ Toledo, Bioinformat Program, Toledo, OH 43606 USA. [Kohl, Matthias] Univ Bayreuth, Dept Math, Bayreuth, Germany. [Li, Jianying] Univ N Carolina, Lineberger Comprehens Canc Ctr, Chapel Hill, NC 27599 USA. [Li, Li] Stanford Univ, Dept Pediat, Stanford, CA 94305 USA. [Li, Menglong] Sichuan Univ, Coll Chem, Chengdu 610064, Sichuan, Peoples R China. [Li, Quan-Zhen] Univ Texas SW Med Ctr Dallas, Dallas, TX 75390 USA. [Mulligan, George J.] Millennium Pharmaceut Inc, Cambridge, MA USA. [Page, Grier P.] RTI Int, Atlanta, GA USA. [Peng, Xuejun] Takeda Global R&D Ctr Inc, Deerfield, IL USA. [Peterson, Ron L.] Novartis Inst Biomed Res, Cambridge, MA USA. [Ren, Yi] Rutgers State Univ, WM Keck Ctr Collaborat Neurosci, Piscataway, NJ USA. [Roter, Alan H.] Entelos Inc, Foster City, CA USA. [Schumacher, Martin M.; Staedtler, Frank] Novartis Pharma AG, Novartis Inst BioMed Res, Biomarker Dev, Basel, Switzerland. [Shambaugh, Joseph D.] Genedata Inc, Lexington, MA USA. [Shippy, Richard] Affymetrix Inc, Santa Clara, CA USA. [Si, Shengzhu] Hefei Teachers Coll, Dept Chem & Chem Engn, Hefei, Anhui, Peoples R China. [Sotiriou, Christos] Inst Jules Bordet, B-1000 Brussels, Belgium. [Turpaz, Yaron] Lilly Singapore Ctr Drug Discovery Immunos, Singapore, Singapore. [Vega, Silvia C.] Microsoft Corp, US Hlth Solut Grp, Redmond, WA 98052 USA. [von Frese, Juergen] Data Anal Solut DA SOL GmbH, Greifenberg, Germany. [Wang, Wei] Cornell Univ, Ithaca, NY USA. [Willey, James C.] Univ Toledo, Dept Med, Div Pulm & Crit Care Med, Toledo, OH 43606 USA. [Wu, Shujian] Bristol Myers Squibb Co, Pennington, NJ USA. [Xiao, Nianqing] OpGen Inc, Gaithersburg, MD USA.\\Shi, LM, US FDA, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA.
    1. Year: 2010
    2. Date: Oct
  2. Journal: Pharmacogenomics Journal
    1. Pages: S5-S16
  4. Type of Article: Article
  5. ISSN: 1470-269X
  1. 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

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  1. Keywords:

External Sources

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  2. DOI: 10.1038/nbt.1665
  3. View record in Web of Science®
  4. WOS: 000285268700003

Library Notes

  1. Fiscal Year: FY2010-2011
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