Biomarkers in breast cancer to monitor minimal residual disease have remained elusive. We hypothesized that genomic analysis of circulating free DNA (cf DNA) 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 cf DNA 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 cf DNA SNP/copy number results also separated presurgical breast cancer patients from the healthy controls, suggesting specific CNVs in cf DNA have clinical significance. We identified focal high-level DNA amplification in paired tumor and cf DNA 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 cf DNA, 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 cf DNA to distinguish between patients with breast cancer and healthy controls during routine follow-up. The genomic profiles of cf DNA infer dormancy/minimal residual disease in the majority of patients on follow-up.

The Cu(I) sensor Mycobacterium tuberculosis CsoR is a founding member of a new metalloregulatory protein family. Here we show that two "atom" substitutions of the Nε2 face of a Cu(I) coordinating histisine-61 allosterically uncouple Cu(I) and DNA binding, with no effect on Cu (I) binding affinity and coordination structure. A model analogous to the allosteric switch mechanism in Staphylococcus aureus CzrA, a zinc sensor protein with a completely different fold, is proposed.Elucidation of structural and dynamical pathways of communication or coupling between ligand binding sites, i.e., classical allostery, is of topical interest and fundamental importance in biological regulation, 1-3 but remains a challenge to detect and quantify. [4][5][6] Metalloregulatory proteins are specialized allosteric proteins that control the intracellular availability of essential transition metal ions by binding a specific metal, which in turn,