We then examined the correlation of CNV, mRNA, and protein expression levels for several key genes for breast cancer biology: EGFR, ERBB2 (HER2), ESR1, GATA3, PGR, PIK3CA, AKT1/2/3, MTOR and TP53. In most cases, we observed consistent relationships between CNV, mRNA, and protein expression levels. Here, EGFR is linked to breast cancer.