Laboratory intercomparison of gene expression assays

C. Badie, S. Kabacik, Y. Balagurunathan, N. Bernard, M. Brengues, G. Faggioni, R. Greither, F. Lista, A. Peinnequin, T. Poyot, F. Herodin, A. Missel, B. Terbrueggen, Frederic Zenhausern, K. Rothkamm, V. Meineke, H. Braselmann, C. Beinke, M. Abend

Research output: Contribution to journalArticle

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Abstract

The possibility of a large-scale acute radiation exposure necessitates the development of new methods that could provide rapid individual dose estimates with high sample throughput. The focus of the study was an intercomparison of laboratories' dose-assessment performances using gene expression assays. Lithium-heparinized whole blood from one healthy donor was irradiated (240 kVp, 1 Gy/min) immediately after venipuncture at approximately 37°C using single X-ray doses. Blood samples to establish calibration curves (0.25-4 Gy) as well as 10 blinded test samples (0.1-6.4 Gy) were incubated for 24 h at 37°C supplemented with an equal volume of medium and 10% fetal calf serum. For quantitative reverse transcription polymerase chain reaction (qRT-PCR), samples were lysed, stored at-20°C and shipped on ice. For the Chemical Ligation Dependent Probe Amplification methodology (CLPA), aliquots were incubated in 2 ml CLPA reaction buffer (DxTerity), mixed and shipped at room temperature. Assays were run in each laboratory according to locally established protocols. The mean absolute difference (MAD) of estimated doses relative to the true doses (in Gy) was calculated. We also merged doses into binary categories reflecting aspects of clinical/diagnostic relevance and examined accuracy, sensitivity and specificity. The earliest reported time on dose estimates was <8 h. The standard deviation of technical replicate measurements in 75% of all measurements was below 11%. MAD values of 0.3-0.5 Gy and 0.8-1.3 Gy divided the laboratories contributions into two groups. These fourfold differences in accuracy could be primarily explained by unexpected variances of the housekeeping gene (P = 0.0008) and performance differences in processing of calibration and blinded test samples by half of the contributing laboratories. Reported gene expression dose estimates aggregated into binary categories in general showed an accuracies and sensitivities of 93-100% and 76-100% for the groups, with low MAD and high MAD, respectively. In conclusion, gene expression-based dose estimates were reported quickly, and for laboratories with MAD between 0.3-0.5 Gy binary dose categories of clinical significance could be discriminated with an accuracy and sensitivity comparable to established cytogenetic assays.

Original languageEnglish (US)
Pages (from-to)138-148
Number of pages11
JournalRadiation Research
Volume180
Issue number2
DOIs
StatePublished - Aug 2013

Fingerprint

gene expression
Gene Expression
dosage
Calibration
Ligation
Phlebotomy
Essential Genes
Ice
estimates
Lithium
Cytogenetics
Reverse Transcription
blood
sensitivity
Buffers
X-Rays
methodology
Sensitivity and Specificity
polymerase chain reaction
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Radiology Nuclear Medicine and imaging
  • Biophysics
  • Radiation

Cite this

Badie, C., Kabacik, S., Balagurunathan, Y., Bernard, N., Brengues, M., Faggioni, G., ... Abend, M. (2013). Laboratory intercomparison of gene expression assays. Radiation Research, 180(2), 138-148. https://doi.org/10.1667/RR3236.1

Laboratory intercomparison of gene expression assays. / Badie, C.; Kabacik, S.; Balagurunathan, Y.; Bernard, N.; Brengues, M.; Faggioni, G.; Greither, R.; Lista, F.; Peinnequin, A.; Poyot, T.; Herodin, F.; Missel, A.; Terbrueggen, B.; Zenhausern, Frederic; Rothkamm, K.; Meineke, V.; Braselmann, H.; Beinke, C.; Abend, M.

In: Radiation Research, Vol. 180, No. 2, 08.2013, p. 138-148.

Research output: Contribution to journalArticle

Badie, C, Kabacik, S, Balagurunathan, Y, Bernard, N, Brengues, M, Faggioni, G, Greither, R, Lista, F, Peinnequin, A, Poyot, T, Herodin, F, Missel, A, Terbrueggen, B, Zenhausern, F, Rothkamm, K, Meineke, V, Braselmann, H, Beinke, C & Abend, M 2013, 'Laboratory intercomparison of gene expression assays', Radiation Research, vol. 180, no. 2, pp. 138-148. https://doi.org/10.1667/RR3236.1
Badie C, Kabacik S, Balagurunathan Y, Bernard N, Brengues M, Faggioni G et al. Laboratory intercomparison of gene expression assays. Radiation Research. 2013 Aug;180(2):138-148. https://doi.org/10.1667/RR3236.1
Badie, C. ; Kabacik, S. ; Balagurunathan, Y. ; Bernard, N. ; Brengues, M. ; Faggioni, G. ; Greither, R. ; Lista, F. ; Peinnequin, A. ; Poyot, T. ; Herodin, F. ; Missel, A. ; Terbrueggen, B. ; Zenhausern, Frederic ; Rothkamm, K. ; Meineke, V. ; Braselmann, H. ; Beinke, C. ; Abend, M. / Laboratory intercomparison of gene expression assays. In: Radiation Research. 2013 ; Vol. 180, No. 2. pp. 138-148.
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