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.
authors.affiliation: National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.forename: Laura H
authors.initials: LH
authors.lastname: Reid
authors.forename: Wendell D
authors.initials: WD
authors.lastname: Jones
authors.forename: Richard
authors.initials: R
authors.lastname: Shippy
authors.forename: Janet A
authors.initials: JA
authors.lastname: Warrington
authors.forename: Shawn C
authors.initials: SC
authors.lastname: Baker
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Collins
authors.forename: Francoise
authors.initials: F
authors.lastname: de Longueville
authors.forename: Ernest S
authors.initials: ES
authors.lastname: Kawasaki
authors.forename: Kathleen Y
authors.initials: KY
authors.lastname: Lee
authors.forename: Yuling
authors.initials: Y
authors.lastname: Luo
authors.forename: Yongming Andrew
authors.initials: YA
authors.lastname: Sun
authors.forename: James C
authors.initials: JC
authors.lastname: Willey
authors.forename: Robert A
authors.initials: RA
authors.lastname: Setterquist
authors.forename: Gavin M
authors.initials: GM
authors.lastname: Fischer
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.forename: Yvonne P
authors.initials: YP
authors.lastname: Dragan
authors.forename: David J
authors.initials: DJ
authors.lastname: Dix
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authors.initials: FW
authors.lastname: Frueh
authors.forename: Frederico M
authors.initials: FM
authors.lastname: Goodsaid
authors.forename: Damir
authors.initials: D
authors.lastname: Herman
authors.forename: Roderick V
authors.initials: RV
authors.lastname: Jensen
authors.forename: Charles D
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authors.lastname: Johnson
authors.forename: Edward K
authors.initials: EK
authors.lastname: Lobenhofer
authors.forename: Raj K
authors.initials: RK
authors.lastname: Puri
authors.forename: Uwe
authors.initials: U
authors.lastname: Schrf
authors.forename: Jean
authors.initials: J
authors.lastname: Thierry-Mieg
authors.forename: Charles
authors.initials: C
authors.lastname: Wang
authors.forename: Mike
authors.initials: M
authors.lastname: Wilson
authors.forename: Paul K
authors.initials: PK
authors.lastname: Wolber
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.forename: Shashi
authors.initials: S
authors.lastname: Amur
authors.forename: Wenjun
authors.initials: W
authors.lastname: Bao
authors.forename: Catalin C
authors.initials: CC
authors.lastname: Barbacioru
authors.forename: Anne Bergstrom
authors.initials: AB
authors.lastname: Lucas
authors.forename: Vincent
authors.initials: V
authors.lastname: Bertholet
authors.forename: Cecilie
authors.initials: C
authors.lastname: Boysen
authors.forename: Bud
authors.initials: B
authors.lastname: Bromley
authors.forename: Donna
authors.initials: D
authors.lastname: Brown
authors.forename: Alan
authors.initials: A
authors.lastname: Brunner
authors.forename: Roger
authors.initials: R
authors.lastname: Canales
authors.forename: Xiaoxi Megan
authors.initials: XM
authors.lastname: Cao
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Cebula
authors.forename: James J
authors.initials: JJ
authors.lastname: Chen
authors.forename: Jing
authors.initials: J
authors.lastname: Cheng
authors.forename: Tzu-Ming
authors.initials: TM
authors.lastname: Chu
authors.forename: Eugene
authors.initials: E
authors.lastname: Chudin
authors.forename: John
authors.initials: J
authors.lastname: Corson
authors.forename: J Christopher
authors.initials: JC
authors.lastname: Corton
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Croner
authors.forename: Christopher
authors.initials: C
authors.lastname: Davies
authors.forename: Timothy S
authors.initials: TS
authors.lastname: Davison
authors.forename: Glenda
authors.initials: G
authors.lastname: Delenstarr
authors.forename: Xutao
authors.initials: X
authors.lastname: Deng
authors.forename: David
authors.initials: D
authors.lastname: Dorris
authors.forename: Aron C
authors.initials: AC
authors.lastname: Eklund
authors.forename: Xiao-hui
authors.initials: XH
authors.lastname: Fan
authors.forename: Hong
authors.initials: H
authors.lastname: Fang
authors.forename: Stephanie
authors.initials: S
authors.lastname: Fulmer-Smentek
authors.forename: James C
authors.initials: JC
authors.lastname: Fuscoe
authors.forename: Kathryn
authors.initials: K
authors.lastname: Gallagher
authors.forename: Weigong
authors.initials: W
authors.lastname: Ge
authors.forename: Lei
authors.initials: L
authors.lastname: Guo
authors.forename: Xu
authors.initials: X
authors.lastname: Guo
authors.forename: Janet
authors.initials: J
authors.lastname: Hager
authors.forename: Paul K
authors.initials: PK
authors.lastname: Haje
authors.forename: Jing
authors.initials: J
authors.lastname: Han
authors.forename: Tao
authors.initials: T
authors.lastname: Han
authors.forename: Heather C
authors.initials: HC
authors.lastname: Harbottle
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Harris
authors.forename: Eli
authors.initials: E
authors.lastname: Hatchwell
authors.forename: Craig A
authors.initials: CA
authors.lastname: Hauser
authors.forename: Susan
authors.initials: S
authors.lastname: Hester
authors.forename: Huixiao
authors.initials: H
authors.lastname: Hong
authors.forename: Patrick
authors.initials: P
authors.lastname: Hurban
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.forename: Hanlee
authors.initials: H
authors.lastname: Ji
authors.forename: Charles R
authors.initials: CR
authors.lastname: Knight
authors.forename: Winston P
authors.initials: WP
authors.lastname: Kuo
authors.forename: J Eugene
authors.initials: JE
authors.lastname: LeClerc
authors.forename: Shawn
authors.initials: S
authors.lastname: Levy
authors.forename: Quan-Zhen
authors.initials: QZ
authors.lastname: Li
authors.forename: Chunmei
authors.initials: C
authors.lastname: Liu
authors.forename: Ying
authors.initials: Y
authors.lastname: Liu
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Lombardi
authors.forename: Yunqing
authors.initials: Y
authors.lastname: Ma
authors.forename: Scott R
authors.initials: SR
authors.lastname: Magnuson
authors.forename: Botoul
authors.initials: B
authors.lastname: Maqsodi
authors.forename: Tim
authors.initials: T
authors.lastname: McDaniel
authors.forename: Nan
authors.initials: N
authors.lastname: Mei
authors.forename: Ola
authors.initials: O
authors.lastname: Myklebost
authors.forename: Baitang
authors.initials: B
authors.lastname: Ning
authors.forename: Natalia
authors.initials: N
authors.lastname: Novoradovskaya
authors.forename: Michael S
authors.initials: MS
authors.lastname: Orr
authors.forename: Terry W
authors.initials: TW
authors.lastname: Osborn
authors.forename: Adam
authors.initials: A
authors.lastname: Papallo
authors.forename: Tucker A
authors.initials: TA
authors.lastname: Patterson
authors.forename: Roger G
authors.initials: RG
authors.lastname: Perkins
authors.forename: Elizabeth H
authors.initials: EH
authors.lastname: Peters
authors.forename: Ron
authors.initials: R
authors.lastname: Peterson
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Philips
authors.forename: P Scott
authors.initials: PS
authors.lastname: Pine
authors.forename: Lajos
authors.initials: L
authors.lastname: Pusztai
authors.forename: Feng
authors.initials: F
authors.lastname: Qian
authors.forename: Hongzu
authors.initials: H
authors.lastname: Ren
authors.forename: Mitch
authors.initials: M
authors.lastname: Rosen
authors.forename: Barry A
authors.initials: BA
authors.lastname: Rosenzweig
authors.forename: Raymond R
authors.initials: RR
authors.lastname: Samaha
authors.forename: Mark
authors.initials: M
authors.lastname: Schena
authors.forename: Gary P
authors.initials: GP
authors.lastname: Schroth
authors.forename: Svetlana
authors.initials: S
authors.lastname: Shchegrova
authors.forename: Dave D
authors.initials: DD
authors.lastname: Smith
authors.forename: Frank
authors.initials: F
authors.lastname: Staedtler
authors.forename: Zhenqiang
authors.initials: Z
authors.lastname: Su
authors.forename: Hongmei
authors.initials: H
authors.lastname: Sun
authors.forename: Zoltan
authors.initials: Z
authors.lastname: Szallasi
authors.forename: Zivana
authors.initials: Z
authors.lastname: Tezak
authors.forename: Danielle
authors.initials: D
authors.lastname: Thierry-Mieg
authors.forename: Karol L
authors.initials: KL
authors.lastname: Thompson
authors.forename: Irina
authors.initials: I
authors.lastname: Tikhonova
authors.forename: Yaron
authors.initials: Y
authors.lastname: Turpaz
authors.forename: Beena
authors.initials: B
authors.lastname: Vallanat
authors.forename: Christophe
authors.initials: C
authors.lastname: Van
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Walker
authors.forename: Sue Jane
authors.initials: SJ
authors.lastname: Wang
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Wang
authors.forename: Russ
authors.initials: R
authors.lastname: Wolfinger
authors.forename: Alex
authors.initials: A
authors.lastname: Wong
authors.forename: Jie
authors.initials: J
authors.lastname: Wu
authors.forename: Chunlin
authors.initials: C
authors.lastname: Xiao
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authors.lastname: Xie
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
authors.forename: Wen
authors.initials: W
authors.lastname: Yang
authors.forename: Liang
authors.initials: L
authors.lastname: Zhang
authors.forename: Sheng
authors.initials: S
authors.lastname: Zhong
authors.forename: Yaping
authors.initials: Y
authors.lastname: Zong
authors.forename: William
authors.initials: W
authors.lastname: Slikker
mesh_terms: D004867:Equipment Design; D019544:Equipment Failure Analysis; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*; D011785:Quality Assurance, Health Care / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014481:United States