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Updated: Dec 14, 2025
Cell-Free DNA Integrity Analysis in Urine Samples
Published on: January 5, 2017
A novel cell-free single-molecule unique primer extension resequencing (cf-SUPER) technology for bladder cancer
Cheng Zhao1,2, Yi Pan3, Yinhuai Wang4
1Department of Urology, the Third Xiangya Hospital, Central South University, Changsha 410013, China.
Background:
The clinical diagnostic method for bladder cancer is cystoscopy, an invasive, expensive and inconvenient clinical test. Using urinary cell-free DNA (cfDNA) to develop non-invasive test for bladder cancer was a promising liquid biopsy.
Methods:
To improve the using rate of cfDNA template and decrease the PCR bias for liquid biopsy using urinary cfDNA, we developed a cell-free single-molecule unique primer extension resequencing (cf-SUPER) technology which was done for 29 matched urinary cfDNA and tumor DNA samples of bladder cancer patients to evaluate consistency of mutation profiles. Then, a 22 high mutational frequence genes was selected to form an uriprier panel, which was analyzed in 100 patients (47 bladder cancer cases and 53 controls) using cf-SUPER technology. This performance of the technology was evaluated using bioinformatic tools and clinical samples.
Results:
The study showed that cf-SUPER technology can accurately detect mutations with allele fractions even low as 0.01% and the DNA input as low as 1 ng. The consistency of mutation profiles and clinical pathological diagnose between 29 matched urinary cfDNA and tumor DNA samples was respectively 82.76% and 89.66% by using cf-SUPER technology. Using cf-SUPER technology, the sensitivity and specificity were 98%, 94% respectively for uriprier panel in non-invasive test.
Conclusions:
The preliminary work shows that cf-SUPER technology will be a promising method for liquid biopsy. Focusing urinary cfDNA, the non-invasive diagnose and monitoring of bladder cancer can come true by using cf-SUPER technology.
