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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
The Microarray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
Nature Biotechnology, Volume 28, No. 8, Year 2010
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Description
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. © 2010 Nature America, Inc. All rights reserved.
Authors & Co-Authors
Shi, Leming
United States, Jeffersonville
National Center for Toxicological Research
Campbell, Gregory A.
United States, Rockville
Food and Drug Administration, Center for Devices and Radiological Health
Jones, Wendell D.
United States, Durham
Expression Analysis
Campagne, Fabien
United States, New York
Weill Cornell Medicine
Wen, Zhining
United States, Jeffersonville
National Center for Toxicological Research
Walker, Stephen J.
United States, Winston Salem
Wake Forest University School of Medicine
Su, Zhenqiang
United States, Silver Spring
Food and Drug Administration
Chu, Tzu Ming
United States, Cary
Sas Institute, Inc.
Goodsaid, Federico M.
United States, Silver Spring
Food and Drug Administration
Pusztai, Lajos
United States, Houston
University of Texas Health Science Center at Houston
Shaughnessy, John D.
United States, Little Rock
University of Arkansas for Medical Sciences
Oberthuer, André
Germany, Koln
Universität zu Köln
Thomas, Russell S.
United States, Research Triangle Park
The Hamner Institutes for Health Sciences
Paules, Richard S.
United States, Research Triangle Park
National Institute of Environmental Health Sciences Niehs
Fielden, Mark
United States, Palo Alto
Roche Palo Alto
Barlogie, Bart M.
United States, Little Rock
University of Arkansas for Medical Sciences
Chen, Weijie
United States, Rockville
Food and Drug Administration, Center for Devices and Radiological Health
Du, Pan
United States, Evanston
Northwestern University
Fischer, Matthias
Germany, Koln
Universität zu Köln
Furlanello, Cesare
Italy, Trento
Bruno Kessler Foundation
Gallas, Brandon D.
United States, Rockville
Food and Drug Administration, Center for Devices and Radiological Health
Ge, Xijin
United States, Brookings
South Dakota State University
Megherbi, Dalila B.
United States, Lowell
University of Massachusetts Lowell
Symmans, William F Frasher
United States, Houston
The University of Texas Md Anderson Cancer Center
Wang, May D.
United States, Atlanta
Emory University
Zhang, John
United States, Waltham
Systems Analytics Inc.
Bitter, Hans
United States, Nutley
Hoffmann-la Roche Inc.
Brors, Benedikt
Germany, Heidelberg
German Cancer Research Center
Bushel, Pierre R.
United States, Research Triangle Park
National Institute of Environmental Health Sciences Niehs
Bylesjo, Max
Sweden, Umea
Umeå Universitet
Chen, Minjun
United States, Jeffersonville
National Center for Toxicological Research
Cheng, Jie
United States, Philadelphia
Glaxosmithkline, Usa
Cheng, Jing
China, Beijing
Tsinghua University Medical Systems Biology Research Center
Chou, Jeff
United States, Research Triangle Park
National Institute of Environmental Health Sciences Niehs
Davison, Timothy S.
United Kingdom, Craigavon
Almac Group Ltd
Delorenzi, Mauro
Switzerland, Lausanne
Sib Swiss Institute of Bioinformatics
Deng, Youping
United States, Hattiesburg
University of Southern Mississippi
Devanarayan, Viswanath
United States, Philadelphia
Abbott Laboratories
Dix, David J.
United States, Washington, D.c.
United States Environmental Protection Agency
Dopazo, Joaquin A.
Spain, Valencia
Centro de Investigacion Principe Felipe
Dorff, Kevin C.
United States, New York
Weill Cornell Medicine
Elloumi, Fathi
United States, Washington, D.c.
United States Environmental Protection Agency
Fan, Jianqing
United States, Princeton
Princeton University
Fan, Shicai
China, Beijing
Tsinghua University
Fan, Xiaohui
China, Hangzhou
College of Pharmaceutical Sciences, Zhejiang University
Fang, Hong
United States, Silver Spring
Food and Drug Administration
Gonzaludo, Nina
United States, Palo Alto
Roche Palo Alto
Hess, Kenneth R.
United States, Houston
The University of Texas Md Anderson Cancer Center
Hong, Huixiao
United States, Jeffersonville
National Center for Toxicological Research
Huan, Jun
United States, Lawrence
University of Kansas
Irizarry, Rafael A.
United States, Baltimore
Johns Hopkins University
Judson, Richard
United States, Washington, D.c.
United States Environmental Protection Agency
Juraeva, Dilafruz
Germany, Heidelberg
German Cancer Research Center
Lababidi, Samir
United States, Bethesda
Fda Center for Biologics Evaluation and Research
Lambert, Christophe Gerard
United States, Bozeman
Golden Helix Incorporated
Li, Li
United States, Cary
Sas Institute, Inc.
Li, Yanen
United States, Urbana
University of Illinois Urbana-champaign
Li, Zhen
United States, Washington, D.c.
United States Environmental Protection Agency
Lin, Simon M.
United States, Evanston
Northwestern University
Liu, Guozhen
United States, Frederick
A Qiagen Company
Lobenhofer, Edward K.
United States, Morrisville
Division of Clinical Data, Inc.
Luo, Jun
United States, Waltham
Systems Analytics Inc.
Luo, Wen
United States, San Diego
Ligand Pharmaceuticals Incorporated
McCall, Matthew N.
United States, Baltimore
Johns Hopkins University
Nikolsky, Yuri
United States, Encinitas
Genego Inc.
Pennello, Gene A.
United States, Rockville
Food and Drug Administration, Center for Devices and Radiological Health
Perkins, Roger G.
United States, Jeffersonville
National Center for Toxicological Research
Philip, Reena
United States, Rockville
Food and Drug Administration, Center for Devices and Radiological Health
Popovici, Vlad
Switzerland, Lausanne
Sib Swiss Institute of Bioinformatics
Price, Nathan D.
United States, Urbana
University of Illinois Urbana-champaign
Qian, Feng
United States, Silver Spring
Food and Drug Administration
Scherer, Andreas
Unknown Affiliation
Shi, Tieliu
China, Shanghai
East China Normal University
Shi, Weiwei
United States, Encinitas
Genego Inc.
Sung, Jaeyun
United States, Urbana
University of Illinois Urbana-champaign
Thierry-Mieg, Danielle
United States, Bethesda
National Institutes of Health Nih
Thierry-Mieg, Jean
United States, Bethesda
National Institutes of Health Nih
Thodima, Venkata
United States, New York
Memorial Sloan-kettering Cancer Center
Trygg, Johan
Sweden, Umea
Umeå Universitet
Vishnuvajjala, Lakshmi
United States, Rockville
Food and Drug Administration, Center for Devices and Radiological Health
Wang, Sue Jane
United States, Silver Spring
Food and Drug Administration
Wu, Jianping
China, Beijing
Capitalbio Corporation
Wu, Yichao
United States, Raleigh
Nc State University
Xie, Qian
United States, Reston
General Dynamics Corporation
Yousef, Waleed A.
Egypt, Helwan
Helwan University
Zhang, Liang
China, Beijing
Capitalbio Corporation
Zhang, Xuegong
China, Beijing
Tsinghua University
Zhong, Sheng
United States, Urbana
University of Illinois Urbana-champaign
Zhou, Yiming
United States, Little Rock
University of Arkansas for Medical Sciences
Zhu, Sheng
China, Beijing
Capitalbio Corporation
Arasappan, Dhivya
United States, Silver Spring
Food and Drug Administration
Bao, Wenjun
United States, Cary
Sas Institute, Inc.
Lucas, Anne Bergstrom
United States, Santa Clara
Agilent Technologies
Berthold, Frank
Germany, Koln
Universität zu Köln
Brennan, Richard J.
United States, Encinitas
Genego Inc.
Buness, Andreas
Switzerland, Basel
F. Hoffmann-la Roche ag
Catalano, Jennifer G.
United States, Bethesda
Fda Center for Biologics Evaluation and Research
Chang, Chang
China, Shanghai
East China Normal University
Chen, Rong
United States, Stanford
Stanford University School of Medicine
Cheng, Yiyu
Russian Federation, Moscow
Vavilov Institute of General Genetics, Russian Academy of Sciences
Statistics
Citations: 499
Authors: 100
Affiliations: 54
Identifiers
Doi:
10.1038/nbt.1665
ISSN:
10870156
e-ISSN:
15461696
Research Areas
Cancer
Genetics And Genomics
Study Design
Phenomenological Study