Supplementary Figures S1-S13 from Cell-Free Urine and Plasma DNA Mutational Analysis Predicts Neoadjuvant Chemotherapy Response and Outcome in Patients with Muscle-Invasive Bladder Cancer

Abstract

<p>Supplementary Fig. 1. Overview of sample availability and in-silico analysis of the limit of detection for the applied methodology.Supplementary Fig. 2. Comparison between mutations observed in primary and residual tumors at radical cystectomy (RC).Supplementary Fig. 3. Mean sample VAF levels for plasma, urine pellet and urine supernatant split by tdDNA call status in other paired sample types from the same clinical visit.Supplementary Fig. 4. Association between mean sample VAF.Supplementary Fig. 5. Association between mean VAFSupplementary Fig. 6. Urine dipstick measurements compared to the amount of DNA extracted from urine supernatants collected at the same time (+/- 1 day).Supplementary Fig. 7. Urine dipstick measurements compared to the urinary tumor DNA (utDNA) call status in urine supernatants collected at the same time (+/- 1 day).Supplementary Fig. 8. Urine dipstick measurements compared to the urinary tumor DNA (utDNA) level in urine supernatants collected at the same time (+/- 1 day).Supplementary Fig. 9. Mean sample VAF levels for all patients with detectable tumor DNA split by sample type. Tumor stage evaluation was based on the TURB specimen and tumor DNA level based on samples collected before TURB.Supplementary Fig. 10. Kaplan-Meier survival analysis of recurrence-free survival (RFS) stratified by tumor DNA status for all sample types.Supplementary Fig. 11. Tumor DNA levels compared to NAC response.Supplementary Fig. 12. Kaplan-Meier survival analysis of recurrence-free survival (RFS) stratified by tumor DNA level for all sample types.Supplementary Fig. 13. a-b) Association between tumor DNA dynamics and neoadjuvant chemotherapy (NAC) response for a) urine pellet and b) urine supernatant. Tumor DNA clearance was defined as tumor DNA going from detectable to non-detectable and tumor DNA remains was defined as tumor DNA remaining detectable. c-d) Kaplan-Meier survival analysis of tumor DNA dynamics groups and recurrence-free survival (RFS) for c) urine pellet and d) urine supernatant.</p>