The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

Leming Shi; Laura H. Reid; Wendell D. Jones; Richard Shippy; Janet A. Warrington; Shawn C. Baker; Patrick J. Collins; Francoise De Longueville; Ernest S. Kawasaki; Kathleen Y. Lee; Yuling Luo; Yongming Andrew Sun; James C. Willey; Robert A. Setterquist; Gavin M. Fischer; Weida Tong; Yvonne P. Dragan; David J. Dix; Felix W. Frueh; Federico M. Goodsaid; Damir Herman; Roderick V. Jensen; Charles D. Johnson; Edward K. Lobenhofer; Raj K. Puri; Uwe Scherf; Jean Thierry-Mieg; Charles Wang; Mike Wilson; Paul K. Wolber; Lu Zhang; William Slikker; Shashi Amur; Wenjun Bao; Catalin C. Barbacioru; Anne Bergstrom Lucas; Vincent Bertholet; Cecilie Boysen; Bud Bromley; Donna Brown; Alan Brunner; Roger Canales; Xiaoxi Megan Cao; Thomas A. Cebula; James J. Chen; Jing Cheng; Tzu Ming Chu; Eugene Chudin; John Corson; J. Christopher Corton; Lisa J. Croner; Christopher Davies; Timothy S. Davison; Glenda Delenstarr; Xutao Deng; David Dorris; Aron C. Eklund; Xiao Hui Fan; Hong Fang; Stephanie Fulmer-Smentek; James C. Fuscoe; Kathryn Gallagher; Weigong Ge; Lei Guo; Xu Guo; Janet Hager; Paul K. Haje; Jing Han; Tao Han; Heather C. Harbottle; Stephen C. Harris; Eli Hatchwell; Craig A. Hauser; Susan Hester; Huixiao Hong; Patrick Hurban; Scott A. Jackson; Hanlee Ji; Charles R. Knight; Winston P. Kuo; J. Eugene LeClerc; Shawn Levy; Quan Zhen Li; Chunmei Liu; Ying Liu; Michael J. Lombardi; Yunqing Ma; Scott R. Magnuson; Botoul Maqsodi; Tim McDaniel; Nan Mei; Ola Myklebost; Baitang Ning; Natalia Novoradovskaya; Michael S. Orr; Terry W. Osborn; Adam Papallo; Tucker A. Patterson; Roger G. Perkins; Elizabeth H. Peters; Ron Peterson; Kenneth L. Philips; P. Scott Pine; Lajos Pusztai; Feng Qian; Hongzu Ren; Mitch Rosen; Barry A. Rosenzweig; Raymond R. Samaha; Mark Schena; Gary P. Schroth; Svetlana Shchegrova; Dave D. Smith; Frank Staedtler; Zhenqiang Su; Hongmei Sun; Zoltan Szallasi; Zivana Tezak; Danielle Thierry-Mieg; Karol L. Thompson; Irina Tikhonova; Yaron Turpaz; Beena Vallanat; Christophe Van; Stephen J. Walker; Sue Jane Wang; Yonghong Wang; Russ Wolfinger; Alex Wong; Jie Wu; Chunlin Xiao; Qian Xie; Jun Xu; Wen Yang; Liang Zhang; Sheng Zhong; Yaping Zong

doi:10.1038/nbt1239

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

Leming Shi, Laura H. Reid, Wendell D. Jones, Richard Shippy, Janet A. Warrington, Shawn C. Baker, Patrick J. Collins, Francoise De Longueville, Ernest S. Kawasaki, Kathleen Y. Lee, Yuling Luo, Yongming Andrew Sun, James C. Willey, Robert A. Setterquist, Gavin M. Fischer, Weida Tong, Yvonne P. Dragan, David J. Dix, Felix W. Frueh, Federico M. GoodsaidDamir Herman, Roderick V. Jensen, Charles D. Johnson, Edward K. Lobenhofer, Raj K. Puri, Uwe Scherf, Jean Thierry-Mieg, Charles Wang, Mike Wilson, Paul K. Wolber, Lu Zhang, William Slikker, Shashi Amur, Wenjun Bao, Catalin C. Barbacioru, Anne Bergstrom Lucas, Vincent Bertholet, Cecilie Boysen, Bud Bromley, Donna Brown, Alan Brunner, Roger Canales, Xiaoxi Megan Cao, Thomas A. Cebula, James J. Chen, Jing Cheng, Tzu Ming Chu, Eugene Chudin, John Corson, J. Christopher Corton, Lisa J. Croner, Christopher Davies, Timothy S. Davison, Glenda Delenstarr, Xutao Deng, David Dorris, Aron C. Eklund, Xiao Hui Fan, Hong Fang, Stephanie Fulmer-Smentek, James C. Fuscoe, Kathryn Gallagher, Weigong Ge, Lei Guo, Xu Guo, Janet Hager, Paul K. Haje, Jing Han, Tao Han, Heather C. Harbottle, Stephen C. Harris, Eli Hatchwell, Craig A. Hauser, Susan Hester, Huixiao Hong, Patrick Hurban, Scott A. Jackson, Hanlee Ji, Charles R. Knight, Winston P. Kuo, J. Eugene LeClerc, Shawn Levy, Quan Zhen Li, Chunmei Liu, Ying Liu, Michael J. Lombardi, Yunqing Ma, Scott R. Magnuson, Botoul Maqsodi, Tim McDaniel, Nan Mei, Ola Myklebost, Baitang Ning, Natalia Novoradovskaya, Michael S. Orr, Terry W. Osborn, Adam Papallo, Tucker A. Patterson, Roger G. Perkins, Elizabeth H. Peters, Ron Peterson, Kenneth L. Philips, P. Scott Pine, Lajos Pusztai, Feng Qian, Hongzu Ren, Mitch Rosen, Barry A. Rosenzweig, Raymond R. Samaha, Mark Schena, Gary P. Schroth, Svetlana Shchegrova, Dave D. Smith, Frank Staedtler, Zhenqiang Su, Hongmei Sun, Zoltan Szallasi, Zivana Tezak, Danielle Thierry-Mieg, Karol L. Thompson, Irina Tikhonova, Yaron Turpaz, Beena Vallanat, Christophe Van, Stephen J. Walker, Sue Jane Wang, Yonghong Wang, Russ Wolfinger, Alex Wong, Jie Wu, Chunlin Xiao, Qian Xie, Jun Xu, Wen Yang, Liang Zhang, Sheng Zhong, Yaping Zong

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Abstract

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.

Original language	English (US)
Pages (from-to)	1151-1161
Number of pages	11
Journal	Nature biotechnology
Volume	24
Issue number	9
DOIs	https://doi.org/10.1038/nbt1239
State	Published - Sep 1 2006

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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10.1038/nbt1239

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Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., Baker, S. C., Collins, P. J., De Longueville, F., Kawasaki, E. S., Lee, K. Y., Luo, Y., Sun, Y. A., Willey, J. C., Setterquist, R. A., Fischer, G. M., Tong, W., Dragan, Y. P., Dix, D. J., Frueh, F. W., ... Zong, Y. (2006). The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature biotechnology, 24(9), 1151-1161. https://doi.org/10.1038/nbt1239

Shi, L, Reid, LH, Jones, WD, Shippy, R, Warrington, JA, Baker, SC, Collins, PJ, De Longueville, F, Kawasaki, ES, Lee, KY, Luo, Y, Sun, YA, Willey, JC, Setterquist, RA, Fischer, GM, Tong, W, Dragan, YP, Dix, DJ, Frueh, FW, Goodsaid, FM, Herman, D, Jensen, RV, Johnson, CD, Lobenhofer, EK, Puri, RK, Scherf, U, Thierry-Mieg, J, Wang, C, Wilson, M, Wolber, PK, Zhang, L, Slikker, W, Amur, S, Bao, W, Barbacioru, CC, Lucas, AB, Bertholet, V, Boysen, C, Bromley, B, Brown, D, Brunner, A, Canales, R, Cao, XM, Cebula, TA, Chen, JJ, Cheng, J, Chu, TM, Chudin, E, Corson, J, Corton, JC, Croner, LJ, Davies, C, Davison, TS, Delenstarr, G, Deng, X, Dorris, D, Eklund, AC, Fan, XH, Fang, H, Fulmer-Smentek, S, Fuscoe, JC, Gallagher, K, Ge, W, Guo, L, Guo, X, Hager, J, Haje, PK, Han, J, Han, T, Harbottle, HC, Harris, SC, Hatchwell, E, Hauser, CA, Hester, S, Hong, H, Hurban, P, Jackson, SA, Ji, H, Knight, CR, Kuo, WP, LeClerc, JE, Levy, S, Li, QZ, Liu, C, Liu, Y, Lombardi, MJ, Ma, Y, Magnuson, SR, Maqsodi, B, McDaniel, T, Mei, N, Myklebost, O, Ning, B, Novoradovskaya, N, Orr, MS, Osborn, TW, Papallo, A, Patterson, TA, Perkins, RG, Peters, EH, Peterson, R, Philips, KL, Pine, PS, Pusztai, L, Qian, F, Ren, H, Rosen, M, Rosenzweig, BA, Samaha, RR, Schena, M, Schroth, GP, Shchegrova, S, Smith, DD, Staedtler, F, Su, Z, Sun, H, Szallasi, Z, Tezak, Z, Thierry-Mieg, D, Thompson, KL, Tikhonova, I, Turpaz, Y, Vallanat, B, Van, C, Walker, SJ, Wang, SJ, Wang, Y, Wolfinger, R, Wong, A, Wu, J, Xiao, C, Xie, Q, Xu, J, Yang, W, Zhang, L, Zhong, S & Zong, Y 2006, 'The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements', Nature biotechnology, vol. 24, no. 9, pp. 1151-1161. https://doi.org/10.1038/nbt1239

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title = "The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements",

abstract = "Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.",

author = "Leming Shi and Reid, {Laura H.} and Jones, {Wendell D.} and Richard Shippy and Warrington, {Janet A.} and Baker, {Shawn C.} and Collins, {Patrick J.} and {De Longueville}, Francoise and Kawasaki, {Ernest S.} and Lee, {Kathleen Y.} and Yuling Luo and Sun, {Yongming Andrew} and Willey, {James C.} and Setterquist, {Robert A.} and Fischer, {Gavin M.} and Weida Tong and Dragan, {Yvonne P.} and Dix, {David J.} and Frueh, {Felix W.} and Goodsaid, {Federico M.} and Damir Herman and Jensen, {Roderick V.} and Johnson, {Charles D.} and Lobenhofer, {Edward K.} and Puri, {Raj K.} and Uwe Scherf and Jean Thierry-Mieg and Charles Wang and Mike Wilson and Wolber, {Paul K.} and Lu Zhang and William Slikker and Shashi Amur and Wenjun Bao and Barbacioru, {Catalin C.} and Lucas, {Anne Bergstrom} and Vincent Bertholet and Cecilie Boysen and Bud Bromley and Donna Brown and Alan Brunner and Roger Canales and Cao, {Xiaoxi Megan} and Cebula, {Thomas A.} and Chen, {James J.} and Jing Cheng and Chu, {Tzu Ming} and Eugene Chudin and John Corson and Corton, {J. Christopher} and Croner, {Lisa J.} and Christopher Davies and Davison, {Timothy S.} and Glenda Delenstarr and Xutao Deng and David Dorris and Eklund, {Aron C.} and Fan, {Xiao Hui} and Hong Fang and Stephanie Fulmer-Smentek and Fuscoe, {James C.} and Kathryn Gallagher and Weigong Ge and Lei Guo and Xu Guo and Janet Hager and Haje, {Paul K.} and Jing Han and Tao Han and Harbottle, {Heather C.} and Harris, {Stephen C.} and Eli Hatchwell and Hauser, {Craig A.} and Susan Hester and Huixiao Hong and Patrick Hurban and Jackson, {Scott A.} and Hanlee Ji and Knight, {Charles R.} and Kuo, {Winston P.} and LeClerc, {J. Eugene} and Shawn Levy and Li, {Quan Zhen} and Chunmei Liu and Ying Liu and Lombardi, {Michael J.} and Yunqing Ma and Magnuson, {Scott R.} and Botoul Maqsodi and Tim McDaniel and Nan Mei and Ola Myklebost and Baitang Ning and Natalia Novoradovskaya and Orr, {Michael S.} and Osborn, {Terry W.} and Adam Papallo and Patterson, {Tucker A.} and Perkins, {Roger G.} and Peters, {Elizabeth H.} and Ron Peterson and Philips, {Kenneth L.} and Pine, {P. Scott} and Lajos Pusztai and Feng Qian and Hongzu Ren and Mitch Rosen and Rosenzweig, {Barry A.} and Samaha, {Raymond R.} and Mark Schena and Schroth, {Gary P.} and Svetlana Shchegrova and Smith, {Dave D.} and Frank Staedtler and Zhenqiang Su and Hongmei Sun and Zoltan Szallasi and Zivana Tezak and Danielle Thierry-Mieg and Thompson, {Karol L.} and Irina Tikhonova and Yaron Turpaz and Beena Vallanat and Christophe Van and Walker, {Stephen J.} and Wang, {Sue Jane} and Yonghong Wang and Russ Wolfinger and Alex Wong and Jie Wu and Chunlin Xiao and Qian Xie and Jun Xu and Wen Yang and Liang Zhang and Sheng Zhong and Yaping Zong",

note = "Publisher Copyright: {\textcopyright} 2006 Nature Publishing Group.",

year = "2006",

month = sep,

day = "1",

doi = "10.1038/nbt1239",

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pages = "1151--1161",

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T1 - The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

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AU - Reid, Laura H.

AU - Jones, Wendell D.

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AU - Warrington, Janet A.

AU - Baker, Shawn C.

AU - Collins, Patrick J.

AU - De Longueville, Francoise

AU - Kawasaki, Ernest S.

AU - Lee, Kathleen Y.

AU - Luo, Yuling

AU - Sun, Yongming Andrew

AU - Willey, James C.

AU - Setterquist, Robert A.

AU - Fischer, Gavin M.

AU - Tong, Weida

AU - Dragan, Yvonne P.

AU - Dix, David J.

AU - Frueh, Felix W.

AU - Goodsaid, Federico M.

AU - Herman, Damir

AU - Jensen, Roderick V.

AU - Johnson, Charles D.

AU - Lobenhofer, Edward K.

AU - Puri, Raj K.

AU - Scherf, Uwe

AU - Thierry-Mieg, Jean

AU - Wang, Charles

AU - Wilson, Mike

AU - Wolber, Paul K.

AU - Zhang, Lu

AU - Slikker, William

AU - Amur, Shashi

AU - Bao, Wenjun

AU - Barbacioru, Catalin C.

AU - Lucas, Anne Bergstrom

AU - Bertholet, Vincent

AU - Boysen, Cecilie

AU - Bromley, Bud

AU - Brown, Donna

AU - Brunner, Alan

AU - Canales, Roger

AU - Cao, Xiaoxi Megan

AU - Cebula, Thomas A.

AU - Chen, James J.

AU - Cheng, Jing

AU - Chu, Tzu Ming

AU - Chudin, Eugene

AU - Corson, John

AU - Corton, J. Christopher

AU - Croner, Lisa J.

AU - Davies, Christopher

AU - Davison, Timothy S.

AU - Delenstarr, Glenda

AU - Deng, Xutao

AU - Dorris, David

AU - Eklund, Aron C.

AU - Fan, Xiao Hui

AU - Fang, Hong

AU - Fulmer-Smentek, Stephanie

AU - Fuscoe, James C.

AU - Gallagher, Kathryn

AU - Ge, Weigong

AU - Guo, Lei

AU - Guo, Xu

AU - Hager, Janet

AU - Haje, Paul K.

AU - Han, Jing

AU - Han, Tao

AU - Harbottle, Heather C.

AU - Harris, Stephen C.

AU - Hatchwell, Eli

AU - Hauser, Craig A.

AU - Hester, Susan

AU - Hong, Huixiao

AU - Hurban, Patrick

AU - Jackson, Scott A.

AU - Ji, Hanlee

AU - Knight, Charles R.

AU - Kuo, Winston P.

AU - LeClerc, J. Eugene

AU - Levy, Shawn

AU - Li, Quan Zhen

AU - Liu, Chunmei

AU - Liu, Ying

AU - Lombardi, Michael J.

AU - Ma, Yunqing

AU - Magnuson, Scott R.

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AU - Mei, Nan

AU - Myklebost, Ola

AU - Ning, Baitang

AU - Novoradovskaya, Natalia

AU - Orr, Michael S.

AU - Osborn, Terry W.

AU - Papallo, Adam

AU - Patterson, Tucker A.

AU - Perkins, Roger G.

AU - Peters, Elizabeth H.

AU - Peterson, Ron

AU - Philips, Kenneth L.

AU - Pine, P. Scott

AU - Pusztai, Lajos

AU - Qian, Feng

AU - Ren, Hongzu

AU - Rosen, Mitch

AU - Rosenzweig, Barry A.

AU - Samaha, Raymond R.

AU - Schena, Mark

AU - Schroth, Gary P.

AU - Shchegrova, Svetlana

AU - Smith, Dave D.

AU - Staedtler, Frank

AU - Su, Zhenqiang

AU - Sun, Hongmei

AU - Szallasi, Zoltan

AU - Tezak, Zivana

AU - Thierry-Mieg, Danielle

AU - Thompson, Karol L.

AU - Tikhonova, Irina

AU - Turpaz, Yaron

AU - Vallanat, Beena

AU - Van, Christophe

AU - Walker, Stephen J.

AU - Wang, Sue Jane

AU - Wang, Yonghong

AU - Wolfinger, Russ

AU - Wong, Alex

AU - Wu, Jie

AU - Xiao, Chunlin

AU - Xie, Qian

AU - Xu, Jun

AU - Yang, Wen

AU - Zhang, Liang

AU - Zhong, Sheng

AU - Zong, Yaping

PY - 2006/9/1

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AB - Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.

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ER -

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

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