Pilot study: Urine cell-free DNA with low-pass whole genome sequencing can detect and molecularly type upper tract urothelial carcinomas.

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Upper tract urothelial carcinoma (UTUC) is an aggressive disease that is challenging to biopsy and diagnose, frequently yielding nondiagnostic cytology and tissue specimens. Therefore, UTUC is often late stage when diagnosed, with poor outcomes. Cell-free tumor DNA (cfDNA) may improve UTUC early diagnosis and assessments of heterogeneity, treatment response, and recurrence but has not been studied in the urine from patients with UTUC. This study aimed to detect recurrent, diagnostic UTUC cytogenetic abnormalities by low-pass whole genome sequencing (LPWGS) and to compare urine-derived and plasma cfDNA against abnormalities identified in patient tumor tissue. Cell-free tumor DNA extracted from voided urine and plasma before nephroureterectomy in 4 patients with UTUC was compared with genomic DNA from formalin-fixed, paraffin-embedded tumor tissue after LPWGS. Abnormal autosomal genomic regions were highest in tissue (n = 11,843), intermediate in urine (n = 5,072) and lowest in plasma (n = 763), with a high concordance of flagged regions identified in tissue and urine (r = 0.88). Pairwise analysis of whole chromosome gains/losses and subchromosomal alterations between tissue and urine showed nearly identical patterns in all 4 patients (r = 0.88-0.99) in contrast to plasma (r < 0.25). Abnormal genomic regions identified by LPWGS showed a high degree of overlap (100% for tumor tissue, 94% for urine cfDNA) with cBioPortal UTUC-associated genes. We demonstrated the superiority of urine vs plasma cfDNA when LPWGS was used to identify UTUC-associated gene abnormalities. Voided urine cfDNA molecular signatures are highly concordant with matched tumor tissue on chromosomal and subchromosomal levels, emphasizing its feasibility as a noninvasive biomarker for UTUC detection and surveillance.