Prediction of breast cancer risk based on flow variant analysis of circulating peripheral blood mononuclear cells

Identifying women at high risk for developing breast cancer is potentially lifesaving. Patients with pathogenic genetic variants can embark on a program of surveillance for early detection, chemoprevention, and/or prophylactic surgery. Newly diagnosed cancer patients can also use the results of gene panel sequencing to make decisions about surgery; therefore, rapid turnaround time for results is critical. Cancer Risk B (CR-B), a test that uses flow variant assays to assess the effects of variants in the DNA double-strand break repair, was applied to two groups of subjects who underwent coincidental gene panel testing, thereby allowing an assessment of sensitivity, specificity and accuracy, and utility for annotating variants of uncertain significance (VUS). The test was compared in matched peripheral blood mononuclear cells (PBMCs) and lymphoblastoid cells (LCLs) and tested for rescue in LCLs with gene transfer. The CR-B phenotype demonstrated a bimodal distribution: CR-B⁺ indicative of DSB repair defects, and CR-B⁻, indicative of wild-type repair. When comparing matched LCLs and PBMCs and inter-day tests, CR-B yielded highly reproducible results. The CR-B⁻ phenotype was rescued by gene transfer using wild-type cDNA expression plasmids. The CR-B⁻ phenotype predicted VUS as benign or likely benign. CR-B could represent a rapid alternative to panel sequencing for women with cancer and identifying women at high risk for cancer and is a useful adjunct for annotating VUS.