Abstract
BackgroundThe present study sought to identify a panel of DNA markers for noninvasive diagnosis using cell-free DNA (cfDNA) from urine supernatant or cellular DNA from urine sediments of hematuria patients. A panel of 48 bladder cancer-specific genes was selected. A next-generation sequencing-based assay with a cfDNA barcode-enabled single-molecule test was employed. Mutation profiles of blood, urine, and tumor sample from 16 bladder cancer patients were compared. Next, urinary cellular DNA and cfDNA were prospectively collected from 125 patients (92 bladder cancer cases and 33 controls) and analyzed using the 48-gene panel. The individual gene markers and combinations of markers were validated according to the pathology results. The mean areas under the receiver operating characteristic (ROC) curves (AUCs) obtained with the various modeling approaches were calculated and compared.ResultsThis pilot study of 16 bladder cancer patients demonstrated that gene mutations in urine supernatant and sediments had better concordance with cancer tissue as compared with plasma. Logistic analyses suggested two powerful combinations of genes for genetic diagnostic modeling: five genes for urine supernatant (TERT, FGFR3, TP53, PIK3CA, and KRAS) and seven genes for urine sediments (TERT, FGFR3, TP53, HRAS, PIK3CA, KRAS, and ERBB2). The accuracy of the five-gene panel and the seven-gene panel in the validation cohort yielded AUCs of 0.94 [95% confidence interval (CI) 0.91–0.97] and 0.91 (95% CI 0.86–0.96), respectively. With the addition of age and gender, the diagnostic power of the urine supernatant five-gene model and the urine sediment seven-gene model improved as the revised AUCs were 0.9656 (95% CI 0.9368–0.9944) and 0.9587 (95% CI 0.9291–0.9883).ConclusionscfDNA from urine bears great diagnostic potential. A five-gene panel for urine supernatant and a seven-gene panel for urine sediments are promising options for identifying bladder cancer in hematuria patients.
Highlights
The present study sought to identify a panel of DNA markers for noninvasive diagnosis using cell-free DNA from urine supernatant or cellular DNA from urine sediments of hematuria patients
DNA mutation screening by cfBEST For detecting low-abundance mutations in cell-free DNA (cfDNA), we developed a robust and versatile next-generation sequencing (NGS)-based cfDNA allelic molecule-counting system termed the cfDNA barcode-enabled single-molecule test
Differences in the overlap of gene mutations observed in urine supernatant, urine sediments, and plasma when compared with bladder cancer tissues The cumulative mutation rates observed in the four types of body fluids/tissue samples from the 16 patients with hematuria were compared
Summary
The present study sought to identify a panel of DNA markers for noninvasive diagnosis using cell-free DNA (cfDNA) from urine supernatant or cellular DNA from urine sediments of hematuria patients. Urine, and tumor sample from 16 bladder cancer patients were compared. Urinary cellular DNA and cfDNA were prospectively collected from 125 patients (92 bladder cancer cases and 33 controls) and analyzed using the 48-gene panel. Cystoscopy is widely accepted as the gold standard for Recent years, liquid biopsy has gained much attention as a non-invasive tool for cancer diagnosis and surveillance using body fluid. Urine cytology and other urinary tests, such as bladder tumor antigen, nuclear matrix protein 22, or fluorescence in situ hybridization can serve as a liquid biopsy in urinary disease. None of these markers have been accepted for diagnosis in routine practice due to the limited
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