Urinary Comprehensive Genomic Profiling Correlates Urothelial Carcinoma Mutations with Clinical Risk and Efficacy of Intervention

Abstract

The clinical standard of care for urothelial carcinoma (UC) relies on invasive procedures with suboptimal performance. To enhance UC treatment, we developed a urinary comprehensive genomic profiling (uCGP) test, UroAmplitude, that measures mutations from tumor DNA present in urine. In this study, we performed a blinded, prospective validation of technical sensitivity and positive predictive value (PPV) using reference standards, and found at 1% allele frequency, mutation detection performs at 97.4% sensitivity and 80.4% PPV. We then prospectively compared the mutation profiles of urine-extracted DNA to those of matched tumor tissue to validate clinical performance. Here, we found tumor single-nucleotide variants were observed in the urine with a median concordance of 91.7% and uCGP revealed distinct patterns of genomic lesions enriched in low- and high-grade disease. Finally, we retrospectively explored longitudinal case studies to quantify residual disease following bladder-sparing treatments, and found uCGP detected residual disease in patients receiving bladder-sparing treatment and predicted recurrence and disease progression. These findings demonstrate the potential of the UroAmplitude platform to reliably identify and track mutations associated with UC at each stage of disease: diagnosis, treatment, and surveillance. Multiple case studies demonstrate utility for patient risk classification to guide both surgical and therapeutic interventions.

Noninvasive Tests for Bladder Cancer Detection and Surveillance: A Systematic Review of Commercially Available Assays

“…The UroAmp test combines next generation DNA sequencing and a machine learning algorithm to identify mutations in 60 genes associated with bladder cancer. The reported sensitivity is 97.4% [ 44 ]. Bladder Care is an assay that measures levels of DNA methylation on three genes with reported sensitivity of 93.5% and specificity of 92.6% [ 45 ].…”

Urinary comprehensive genomic profiling predicts urothelial carcinoma recurrence and identifies responders to intravesical therapy

“…PIK3CA and TSC1 were also repeatedly mutated and enriched specifically in IVT Refractory patients, each presenting in 25% of patients in the group. Though FGFR3 is one of the most common mutations in UC and a clear candidate gene for targeted therapies, it is preferentially enriched in LG disease [ 28 , 33 ]. Consistent with this, FGFR3 mutations were relatively rare in our cohort (6%), and they were never observed in IVT Refractory patients.…”

“…Therefore, recurrence and progression risk are not derived strictly from the visually apparent tumor removed during TURBT. Notably, the uCGP technology used here was previously validated to accurately genotype bladder tumors from urine collections taken prior to TURBT [ 33 ], so the same technology could be used in a tumor‐informed MRD approach if a urine sample is collected prior to resection. However, that same study demonstrated the mutation heterogeneity derived from bladder field defects that appear concurrent with a primary tumor.…”

“…UroAmp risk algorithms are calculated independent of any clinical features. UroAmp testing methodology was performed as previously described [ 33 ].…”