Targeted Sequencing of Plasma-Derived vs. Urinary cfDNA from Patients with Triple-Negative Breast Cancer

SIMPLE SUMMARY: Circulating cell-free DNA displays vast potential to capture the entire genetic landscape of a tumor and to characterize intratumoral heterogeneity, providing a minimally invasive alternative to tissue biopsy. Several studies have demonstrated the potential of cell-free DNA in the plasma of breast cancer patients. In contrast, very little is known about the utility of urine as an even more patient-convenient analyte for these applications. In this pilot study, we investigated plasma-derived and matching urinary cell-free DNA samples obtained from 15 presurgical triple-negative breast cancer patients using a targeted sequencing approach to identify breast-cancer-related genetic alterations in both body fluids. Taken together, our results indicated that both body fluids appear to be valuable sources bearing complementary information concerning the genetic tumor profile, which might be relevant for disease monitoring and individual treatment decisions. ABSTRACT: In breast cancer, the genetic profiling of circulating cell-free DNA (cfDNA) from blood plasma was shown to have good potential for clinical use. In contrast, only a few studies were performed investigating urinary cfDNA. In this pilot study, we analyzed plasma-derived and matching urinary cfDNA samples obtained from 15 presurgical triple-negative breast cancer patients. We used a targeted next-generation sequencing approach to identify and compare genetic alterations in both body fluids. The cfDNA concentration was higher in urine compared to plasma, but there was no significant correlation between matched samples. Bioinformatical analysis revealed a total of 3339 somatic breast-cancer-related variants (VAF ≥ 3%), whereof 1222 vs. 2117 variants were found in plasma-derived vs. urinary cfDNA, respectively. Further, 431 shared variants were found in both body fluids. Throughout the cohort, the recovery rate of plasma-derived mutations in matching urinary cfDNA was 47% and even 63% for pathogenic variants only. The most frequently occurring pathogenic and likely pathogenic mutated genes were NF1, CHEK2, KMT2C and PTEN in both body fluids. Notably, a pathogenic CHEK2 (T519M) variant was found in all 30 samples. Taken together, our results indicated that body fluids appear to be valuable sources bearing complementary information regarding the genetic tumor profile.