Use of a mixed tissue RNA design for performance assessments on multiple microarray formats.
The comparability and reliability of data generated using microarray technology would be enhanced by use of a common set of standards that allow accuracy, reproducibility and dynamic range assessments on multiple formats. We designed and tested a complex biological reagent for performance measurements on three commercial oligonucleotide array formats that differ in probe design and signal measurement methodology. The reagent is a set of two mixtures with different proportions of RNA for each of four rat tissues (brain, liver, kidney and testes). The design provides four known ratio measurements of >200 reference probes, which were chosen for their tissue-selectivity, dynamic range coverage and alignment to the same exemplar transcript sequence across all three platforms. The data generated from testing three biological replicates of the reagent at eight laboratories on three array formats provides a benchmark set for both laboratory and data processing performance assessments. Close agreement with target ratios adjusted for sample complexity was achieved on all platforms and low variance was observed among platforms, replicates and sites. The mixed tissue design produces a reagent with known gene expression changes within a complex sample and can serve as a paradigm for performance standards for microarrays that target other species.
Thompson
Karol L
KL
Center for Drug Evaluation and Research, US FDA, Silver Spring, MD 20993, USA. karol.thompson@fda.hhs.gov
Rosenzweig
Barry A
BA
Pine
P Scott
PS
Retief
Jacques
J
Turpaz
Yaron
Y
Afshari
Cynthia A
CA
Hamadeh
Hisham K
HK
Damore
Michael A
MA
Boedigheimer
Michael
M
Blomme
Eric
E
Ciurlionis
Rita
R
Waring
Jeffrey F
JF
Fuscoe
James C
JC
Paules
Richard
R
Tucker
Charles J
CJ
Fare
Thomas
T
Coffey
Ernest M
EM
He
Yudong
Y
Collins
Patrick J
PJ
Jarnagin
Kurt
K
Fujimoto
Susan
S
Ganter
Brigitte
B
Kiser
Gretchen
G
Kaysser-Kranich
Tamma
T
Sina
Joseph
J
Sistare
Frank D
FD
D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards*; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards*; D015345:Oligonucleotide Probes; D012333:RNA, Messenger / Q000378:metabolism / Q000592:standards*; D051381:Rats; D017207:Rats, Sprague-Dawley; D012015:Reference Standards; D015203:Reproducibility of Results; D014018:Tissue Distribution
D015345:Oligonucleotide Probes; D012333:RNA, Messenger