A molecular portrait of circulating free DNA of patients with breast cancer: High-resolution analysis using SNP 6.0 arrays.

Abstract

555 Background: Early detection and monitoring the progress of common cancers is a continuing problem. Patients with cancer are known to have cancer-derived DNA circulating free in plasma (cfDNA) and we hypothesised that this may form the basis for a means of detecting and monitoring the disease Methods: For the first time, we have characterised cfDNA of breast cancer patients to create a molecular portrait, using high resolution analysis with Affymetrix SNP 6.0 Arrays. This array features 906,600 probes for single nucleotide polymorphisms (SNPs) and 946,000 probes for copy number variation (CNV) detection and represents more genetic variation on a single array than any other array platform. SNP 6.0 profiles of the primary tumour were compared with paired cfDNA samples of 50 breast cancer patients on follow-up after surgical removal of their primary tumour and related to cfDNA results of 15 primary breast cancer patients for whom we collected pre-surgical blood samples and healthy female controls. Results: Concordance of SNP genotype calls distinguished between breast cancer patients and healthy controls (p < 0.0001) and between pre-operative patients and patients on follow-up who had surgery and treatment (p = 0.002). Principal component analysis of plasma SNP/copy number results also separated 15 pre-surgical breast cancer patients from the healthy controls suggesting CNVs in plasma DNA have clinical significance. In the 50 patients on follow-up specific CNVs were detected in plasma, mirroring the primary tumour, up to 10 years after diagnosis despite no other evidence of disease on routine scanning. Finally, we identified focal high level DNA amplification, clustered at 7 chromosome arms, amenable to high throughput approaches for screening and monitoring. Conclusions: This study clearly demonstrates the potential of SNP/CNV analysis of cfDNA to reliably distinguish between patients with primary breast cancer and healthy controls, and for monitoring patients after the completion of surgery, radiation therapy and chemotherapy. Our findings may also apply to other cancers where early detection is essential for cure and dormancy is a feature.