Data from Noninvasive Detection of <i>HER2</i> Amplification with Plasma DNA Digital PCR

Abstract

<div>Abstract<p><b>Purpose:</b> Digital PCR is a highly accurate method of determining DNA concentration. We adapted digital PCR to determine the presence of oncogenic amplification through noninvasive analysis of circulating free plasma DNA and exemplify this approach by developing a plasma DNA digital PCR assay for <i>HER2</i> copy number.</p><p><b>Experimental Design:</b> The reference gene for copy number assessment was assessed experimentally and bioinformatically. Chromosome 17 pericentromeric probes were shown to be suboptimal, and <i>EFTUD2</i> at chromosome position 17q21.31 was selected for analysis. Digital PCR assay parameters were determined on plasma samples from a development cohort of 65 patients and assessed in an independent validation cohort of plasma samples from 58 patients with metastatic breast cancer. The sequential probability ratio test was used to assign the plasma DNA digital PCR test as being HER2-positive or -negative in the validation cohort.</p><p><b>Results:</b> In the development cohort, the <i>HER2</i>:<i>EFTUD2</i> plasma DNA copy number ratio had a receiver operator area under the curve (AUC) = 0.92 [95% confidence interval (CI), 0.86–0.99, <i>P</i> = 0.0003]. In the independent validation cohort, 64% (7 of 11) of patients with <i>HER2</i>-amplified cancers were classified as plasma digital PCR <i>HER2</i>–positive and 94% (44 of 47) of patients with <i>HER2</i>-nonamplified cancers were classified as digital PCR <i>HER2</i>–negative, with a positive and negative predictive value of 70% and 92%, respectively.</p><p><b>Conclusion:</b> Analysis of plasma DNA with digital PCR has the potential to screen for the acquisition of <i>HER2</i> amplification in metastatic breast cancer. This approach could potentially be adapted to the analysis of any locus amplified in cancer. <i>Clin Cancer Res; 19(12); 3276–84. ©2013 AACR</i>.</p></div>