, Volume 137, Issue 2, pp 647-651
Date: 19 Dec 2012

Comments on the use of a single or multiple probe-set approach for microarray-based analyses of routine molecular markers in breast cancer

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To the Editor,

In a recent paper, Spyratos et al. [1] dealt with the relevant issue of the routine use of DNA-microarray-based analyses as alternative method to evaluate molecular markers in breast cancer. In particular, they tested the reliability of single Affymetrix probe-sets, in evaluating the performance of microarray data for prediction of estrogen (ER), progesterone receptor (PR), and HER2 status (as determined by immunohistochemistry). Since not all Affymetrix probe-sets are equivalent for a given gene, they separately analyzed each probe-set for each gene and compared microarray data to quantitative RT-PCR results of 45 genes including ESR1, PGR, and ERBB2 (respectively coding for ER, PR, and HER2 protein). As expected, they confirmed the unequal quality of quantification of the different probe-sets for ESR1 (9 probe-sets), PGR (2 probe-sets), and ERBB2 (3 probe-sets) by comparison to protein expression. As a similar result was observed for other 42 genes analyzed, they conclu ...