Detection of gene amplification in matched tumour and plasma DNA from breast cancer patients by quantitative PCR

The aim of the present study was to determine whether tumour-specific gene amplification is detectable in circulating cell-free DNA isolated from the plasma of breast cancer patients. Four loci, known to show amplification in breast cancers, were chosen for investigation of paired plasma and tumour DNA: Her-2 and C35 on chromosome 17, and FGFR1 and RAB11f1P1, which map to chromosome 8. Both gene pairs are frequently, but not exclusively, coamplified in breast tumours.

Lymphocyte, tumour and plasma DNA from 21 unselected breast cancer cases were analysed for amplification by a real-time quantitative PCR assay. Primers and a minor groove binder (MGB) TaqMan probe were targeted to the four genes and to an unamplified reference gene selected from each of the two intervals (CNTNAP1 and UNC5ND, respectively). A normal lymphocyte DNA sample was included in each experiment to examine interassay reproducibility and as an experimental calibrator. A ratio above 2.0 was regarded as positive for gene amplification [1].

Amplification was detected in tumour and plasma DNA at all four loci, with frequencies ranging from 19.1% to 52.3%. Five of 21 cases showed concordant amplification of Her-2 in plasma and tumour DNA, compared with four, one and two of 21 cases for C35, FGFR1 and RAB11f1P1 amplification, respectively. No amplification was seen in the lymphocyte DNA samples.

Taken together, these data confirm that tumour-specific amplification, including Her-2 amplification, is detectable in circulating cell-free DNA isolated from the plasma of breast cancer patients. This suggests the possibility of developing a rapid and simple blood screening tool for identification of gene amplification in breast cancer cases.