Evaluation of external RNA controls for the assessment of microarray performance.
External RNA controls (ERCs), although important for microarray assay performance assessment, have yet to be fully implemented in the research community. As part of the MicroArray Quality Control (MAQC) study, two types of ERCs were implemented and evaluated; one was added to the total RNA in the samples before amplification and labeling; the other was added to the copyRNAs (cRNAs) before hybridization. ERC concentration-response curves were used across multiple commercial microarray platforms to identify problematic assays and potential sources of variation in the analytical process. In addition, the behavior of different ERC types was investigated, resulting in several important observations, such as the sample-dependent attributes of performance and the potential of using these control RNAs in a combinatorial fashion. This multiplatform investigation of the behavior and utility of ERCs provides a basis for articulating specific recommendations for their future use in evaluating assay performance across multiple platforms.
Tong
Weida
W
National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. weida.tong@fda.hhs.gov
Lucas
Anne Bergstrom
AB
Shippy
Richard
R
Fan
Xiaohui
X
Fang
Hong
H
Hong
Huixiao
H
Orr
Michael S
MS
Chu
Tzu-Ming
TM
Guo
Xu
X
Collins
Patrick J
PJ
Sun
Yongming Andrew
YA
Wang
Sue-Jane
SJ
Bao
Wenjun
W
Wolfinger
Russell D
RD
Shchegrova
Svetlana
S
Guo
Lei
L
Warrington
Janet A
JA
Shi
Leming
L
D000465:Algorithms; D019544:Equipment Failure Analysis / Q000379:methods*; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000592:standards*; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000592:standards*; D012313:RNA / Q000032:analysis* / Q000235:genetics* / Q000592:standards; D012016:Reference Values; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014481:United States
D012313:RNA