Major Impact of Sampling Methodology on Gene Expression in Estrogen Receptor-Positive Breast Cancer.

To investigate the impact of sampling methodology on gene expression data from primary estrogen receptor-positive (ER+) breast cancer biopsies, global gene expression was measured in core-cut biopsies at baseline and surgery from patients randomly assigned to receive either two weeks of presurgical aromatase inhibitor (AI; n = 157) or no presurgical treatment (n = 56). Those genes most markedly altered in the AI group (eg, , , , ) were similarly altered in the no treatment group; some widely investigated genes that were apparently unaffected in the AI group (eg, ) were counter-altered in the control group, masking actual AI-dependent changes. In the absence of a control group, these artefactual changes would likely lead to the most affected genes being the erroneous focus of research. The findings are likely relevant to all archival collections of ER+ breast cancer.