We compared contactin-associated protein 1 (CNTNAP1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ribonuclease P RNA component H1 (RPPH1) as unamplified reference genes and showed that all three were appropriate for measuring HER2 amplification using breast cancer cell lines and normal DNA controls. The gene discussed is CNTNAP1; the disease is breast cancer.