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A comparison of the accuracy of Illumina HumanHT-12 v3 Expression BeadChip and TaqMan qRT-PCR gene expression results in patient samples from the Tampere Vascular Study

Research output: Contribution to journalArticleScientificpeer-review


Original languageEnglish
Pages (from-to)149-152
Number of pages4
Issue number1
Publication statusPublished - Jan 2013
Publication typeA1 Journal article-refereed


Aims: This study was set up to compare the accuracy, sensitivity and specificity of gene expression results between the Illumina HumanHT-12 v3 Expression BeadChip (GWE) and the TaqMan qRT-PCR low-density array (LDA) in atherosclerotic plaques. Methods: Gene expression levels of 196 genes were determined from 22 atherosclerotic samples and 6 controls with both the GWE and the LDA. Results: The accuracies of GWE in comparison to that of qRT-PCR for absolute fold changes (FC) 1.2, 1.6, 2.0 and 3.0 between cases and controls were 73.5%, 79.1%, 72.4% and 60.7%, respectively. The correlation of expression measurements between these methods was good (r = 0.87, y = 0.151 + 0.586. x), and the Bland-Altman plot showed that for highly up- or down-regulated transcripts, GWE yields lower absolute FC values than LDA. Conclusion: Gene expression results obtained with the GWE are replicated with high accuracy in LDA, even for technically demanding atherosclerotic samples.


  • Accuracy, Atherosclerosis, Genome-wide expression array, Polymerase chain reaction, Sensitivity, Specificity