Utilizing Cell-Free Urinary and Plasma Tumor DNA to Predict Pathologic Stage at Radical Cystectomy
Objective To assess the ability of cell-free urinary and plasma tumor DNA (cfDNA) to predict pathologic stage at
radical cystectomy for patients with clinical muscle-invasive bladder cancer.
Methods A total of 25 patients with clinical muscle-invasive bladder cancer were enrolled before undergoing radical
cystectomy. Blood and urine were collected before surgery. The 600-gene PredicineATLAS panel was used to sequence
blood buffy-coat germline DNA, plasma cfDNA, and urine cfDNA samples. Low-pass whole genome sequencing was
performed on plasma- and urine-derived cfDNA. CfDNA tumor fraction (TF), genome-wide copy number burden
(CNB), and estimated tumor mutational burden (TMB) were measured in both plasma and urine samples and their
correlation with pathologic T-stage was examined.
Results Three of 25 plasma samples had insufficient cfDNA. In 22 of 22 plasma samples and 24 of 25 urine samples,
at least one nonsynonymous somatic variant was detected. Across the cohort, 44% of plasma variants were concordant
with paired urine variants. The mean number of variants did not differ between noninvasive (< pT1/pN0) and invasive
disease (≥ pT1 or N+) for both plasma (8 vs. 9.5 variants; P = 0.85) and urine (33.7 vs. 30 variants; P = 0.45). A strong
correlation was observed between urine TF and urine CNB score within patients (rv = 0.92). Plasma TF (r = 0.38),
urine TF (r = 0.21), and urine CNB score (r = 0.16) exhibited positive correlations with pT stage. Patients with
carcinoma in situ (CIS) had higher mean urine TF and CNB scores ( P = 0.07 and P = 0.05, respectively). Plasma TF
and CNB score did not correlate with the presence of CIS.
Conclusions Combining plasma- and urine-based cfDNA analysis may help identify patients with residual disease
at radical, although we were unable to predict pathologic T-stage based on these metrics.The presence of CIS may
contribute to greater urinary CNB and TF levels. Considering CIS in the analysis may improve the ability to correlate
tumor metrics with pathologic stage. Low-pass whole genome sequencing–derived urinary CNB correlates strongly
with urinary TF and may provide a less resource-intensive method for future longitudinal disease monitoring.
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