title: Intraplatform reproducibility and technical precision of gene expression profiling in 4 laboratories investigating 160 leukemia samples: the DACH study.
abstract: 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.
authors: Munich Leukemia Laboratory, Munich, Germany. alexander.kohlmann@mll-online.com
authors: Alexander
authors: A
authors: Kohlmann
authors: Elisabeth
authors: E
authors: Haschke-Becher
authors: Barbara
authors: B
authors: Wimmer
authors: Ariana
authors: A
authors: Huber-Wechselberger
authors: Sandrine
authors: S
authors: Meyer-Monard
authors: Heike
authors: H
authors: Huxol
authors: Uwe
authors: U
authors: Siegler
authors: Michel
authors: M
authors: Rossier
authors: Thomas
authors: T
authors: Matthes
authors: Michela
authors: M
authors: Rebsamen
authors: Alberto
authors: A
authors: Chiappe
authors: Adeline
authors: A
authors: Diemand
authors: Sonja
authors: S
authors: Rauhut
authors: Andrea
authors: A
authors: Johnson
authors: Wei-Min
authors: WM
authors: Liu
authors: P Mickey
authors: PM
authors: Williams
authors: Lothar
authors: L
authors: Wieczorek
authors: Torsten
authors: T
authors: Haferlach
mesh_terms: D020869:Gene Expression Profiling; D006801:Humans; D007753:Laboratories / Q000592:standards*; D007938:Leukemia / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results