DNA Methylation Markers for Breast Cancer Detection in the Developing World

Purpose: An unmet need in low resource countries is an automated breast cancer-detection assay to prioritize women who should undergo core breast biopsy and pathological review. Therefore, we sought to identify and validate a panel of methylated DNA markers to discriminate between cancer and benign breast lesions using cells obtained by fine needle aspiration (FNA). Experimental Design: Two case-control studies were conducted comparing cancer and benign breast tissue identified from clinical repositories in the U.S., China, and South Africa for marker selection/training (N=226) and testing (N=246). Twenty-five methylated markers were assayed by quantitative multiplex-methylation-specific PCR (QM-MSP) to select and test a cancer-specific panel. Next, a pilot study was conducted on archival FNAs (49 benign, 24 invasive) from women with mammographically suspicious lesions using a newly developed, 5-hour, quantitative, automated cartridge system. We calculated sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) compared to histopathology for the marker panel. Results: In the discovery cohort, 10/25 markers were selected that were highly methylated in breast cancer compared to benign tissues by QM-MSP. In the independent test cohort, this panel yielded an AUC of 0.937 (95% CI = 0.900-0.970). In the FNA pilot, we achieved an AUC of 0.960 (95% CI = 0.883-1.0) using the automated cartridge system. Conclusions: We developed and piloted a fast, and accurate methylation marker-based automated cartridge system to detect breast cancer in FNA samples. This quick ancillary test has the potential to prioritize cancer over benign tissues for expedited pathologic evaluation in poorly resourced countries.