Intraplatform reproducibility and technical precision of gene expression profiling in 4 laboratories investigating 160 leukemia samples: the DACH study.
BACKGROUND
Gene expression profiling has the potential to offer consistent, objective diagnostic test results once a standardized protocol has been established. We investigated the robustness, precision, and reproducibility of microarray technology.


METHODS
One hundred sixty individual patient samples representing 11 subtypes of acute and chronic leukemias, myelodysplastic syndromes, and nonleukemia as a control group were centrally collected and diagnosed as part of the daily routine in the Munich Leukemia Laboratory. The custom AmpliChip Leukemia research microarray was used for technical analyses of quadruplicate mononuclear cell lysates in 4 different laboratories in Germany (D), Austria (A), and Switzerland (CH) (the DACH study).


RESULTS
Total-RNA preparations were successfully performed in 637 (99.5%) of 640 cases. Mean differences between pairs of laboratories in the total-RNA yield from the same sample ranged from 0.02 mug to 1.03 mug. Further processing produced 622 successful in vitro transcription reactions (97.6%); the mean differences between laboratories in the cRNA yield from the same sample ranged from 0.40 mug to 6.18 mug. After hybridization to microarrays, a mean of 47.6%, 46.5%, 46.2%, and 46.4% of probe sets were detected as present for the 4 laboratories, with mean signal-intensity scaling factors of 3.1, 3.7, 4.0, and 4.2, respectively. In unsupervised hierarchical cluster and principal component analyses, replicates from the same patient always clustered closely together, with no indications of any association between gene expression profiles due to different operators or laboratories.


CONCLUSIONS
Microarray analysis can be performed with high interlaboratory reproducibility and with comparable quality and high technical precision across laboratories.
Kohlmann
Alexander
A
Munich Leukemia Laboratory, Munich, Germany. alexander.kohlmann@mll-online.com
Haschke-Becher
Elisabeth
E
Wimmer
Barbara
B
Huber-Wechselberger
Ariana
A
Meyer-Monard
Sandrine
S
Huxol
Heike
H
Siegler
Uwe
U
Rossier
Michel
M
Matthes
Thomas
T
Rebsamen
Michela
M
Chiappe
Alberto
A
Diemand
Adeline
A
Rauhut
Sonja
S
Johnson
Andrea
A
Liu
Wei-Min
WM
Williams
P Mickey
PM
Wieczorek
Lothar
L
Haferlach
Torsten
T
D020869:Gene Expression Profiling; D006801:Humans; D007753:Laboratories / Q000592:standards*; D007938:Leukemia / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results