Robust interlaboratory reproducibility of a gene expression signature measurement consistent with the needs of a new generation of diagnostic tools.
BACKGROUND
The increasing use of DNA microarrays in biomedical research, toxicogenomics, pharmaceutical development, and diagnostics has focused attention on the reproducibility and reliability of microarray measurements. While the reproducibility of microarray gene expression measurements has been the subject of several recent reports, there is still a need for systematic investigation into what factors most contribute to variability of measured expression levels observed among different laboratories and different experimenters.


RESULTS
We report the results of an interlaboratory comparison of gene expression array measurements on the same microarray platform, in which the RNA amplification and labeling, hybridization and wash, and slide scanning were each individually varied. Identical input RNA was used for all experiments. While some sources of variation have measurable influence on individual microarray signals, they showed very low influence on sample-to-reference ratios based on averaged triplicate measurements in the two-color experiments. RNA labeling was the largest contributor to interlaboratory variation.


CONCLUSIONS
Despite this variation, measurement of one particular breast cancer gene expression signature in three different laboratories was found to be highly robust, showing a high intralaboratory and interlaboratory reproducibility when using strictly controlled standard operating procedures.
Ach
Robert A
RA
Molecular Technology Lab, Agilent Laboratories, Agilent Technologies, Santa Clara, CA 95051, USA. robert_ach@agilent.com
Floore
Arno
A
Curry
Bo
B
Lazar
Vladimir
V
Glas
Annuska M
AM
Pover
Rob
R
Tsalenko
Anya
A
Ripoche
Hugues
H
Cardoso
Fatima
F
d'Assignies
Mahasti Saghatchian
MS
Bruhn
Laurakay
L
Van't Veer
Laura J
LJ
D000704:Analysis of Variance; D001943:Breast Neoplasms / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D012313:RNA / Q000302:isolation & purification*; D015203:Reproducibility of Results
D012313:RNA