Comparison of mRNA abundance quantified by gene expression profiling and percentage of positive cells using immunophenotyping for diagnostic antigens in acute and chronic leukemias.

Background: Microarray analysis is considered a future diagnostic tool in leukemias. Whereas data accumulate on specific gene expression patterns in biologically defined leukemia entities, data on the correlation between flow cytometrically determined protein expression, which are essential in the diagnostic setting today, and microarray results are limited.

Methods: The results obtained by microarray analysis were compared using the Affymetrix GeneChip HG-U133 system in parallel with flow cytometric findings of 36 relevant targets in 814 patients with newly diagnosed acute and chronic leukemias as well as in normal bone marrow samples.

Results: In a total of 21,581 individual comparisons between signal intensities obtained by microarray analysis and percentages of positive cell as determined by flow cytometry, coefficients of correlation in the range of 0.171 to 0.807 were obtained. In particular, the degree of correlation was high in the following genes critical in the diagnostic setting: CD4, CD8, CD13 (ANPEP), CD33, CD23 (FCER2), CD64 (FCGR1A), CD117 (KIT), CD34, MPO, CD20 (MS4A1), CD7 (range of r, 0.589-0.807).

Conclusions: The present data prove the high degree of correlation between findings obtained by microarray analysis and flow cytometry. They are in favor of a future application of the microarray technology as a robust diagnostic tool in leukemias.