Genomic analysis of circulating cell-free DNA infers breast cancer dormancy.

Biomarkers in breast cancer to monitor minimal residual disease have remained elusive. We hypothesized that genomic analysis of circulating free DNA (cfDNA) isolated from plasma may form the basis for a means of detecting and monitoring breast cancer. We profiled 251 genomes using Affymetrix SNP 6.0 arrays to determine copy number variations (CNVs) and loss of heterozygosity (LOH), comparing 138 cfDNA samples with matched primary tumor and normal leukocyte DNA in 65 breast cancer patients and eight healthy female controls. Concordance of SNP genotype calls in paired cfDNA and leukocyte DNA samples distinguished between breast cancer patients and healthy female controls (P < 0.0001) and between preoperative patients and patients on follow-up who had surgery and treatment (P = 0.0016). Principal component analyses of cfDNA SNP/copy number results also separated presurgical breast cancer patients from the healthy controls, suggesting specific CNVs in cfDNA have clinical significance. We identified focal high-level DNA amplification in paired tumor and cfDNA clustered in a number of chromosome arms, some of which harbor genes with oncogenic potential, including USP17L2 (DUB3), BRF1, MTA1, and JAG2. Remarkably, in 50 patients on follow-up, specific CNVs were detected in cfDNA, mirroring the primary tumor, up to 12 yr after diagnosis despite no other evidence of disease. These data demonstrate the potential of SNP/CNV analysis of cfDNA to distinguish between patients with breast cancer and healthy controls during routine follow-up. The genomic profiles of cfDNA infer dormancy/minimal residual disease in the majority of patients on follow-up.

Measurements of EGFR expression on circulating tumor cells are reproducible over time in metastatic breast cancer patients.

AIMS: Studies of EGFR expression in breast cancer have shown inconsistent results due in part to a large range of methods used. Anti-EGFR therapy trials have often not used patient selection because of this. We describe the use of the CellSearch system (Veridex LLC, NJ, USA) to enumerate and measure EGFR expression on the surface of circulating tumor cells (CTCs), derived from the peripheral blood of individuals with metastatic breast cancer over time. MATERIALS & METHODS: The CellSearch system was used to quantify CTCs and EGFR measurement was performed on all samples. The specificity of EGFR phenotyping was further examined by spiking with cell lines with increased and low (or absent) levels of EGFR expression using the CellSearch system to enrich and phenotype the CTCs. RESULTS: Serial samples were obtained from 33 individuals with metastatic breast cancer. CTCs derived from these individuals had consistent levels of EGFR expression at different time points, and none of the patients 'switched' from a positive to negative EGFR phenotype or vice versa. The specificity of EGFR phenotyping by the CellSearch system was verified by staining of EGFR only being present in a high EGFR expressing EGFR cell line (MDA-MB-468), as confirmed by Western blotting. CONCLUSIONS: Measurement of EGFR on the surface of CTCs, derived from individuals with metastatic breast cancer patients is possible using the CellSearch system and showed consistent positivity over time. The use of this system will now be validated in a prospective study aiming to identify patients for anti-EGFR therapy based on the expression profile of CTCs.