Genomic Alterations in Liquid Biopsies from Patients with Bladder Cancer

Abstract

Background: At least half of the patients diagnosed with non-muscle-invasive bladder cancer (NMIBC) experience recurrence and approximately 15% will develop progression to muscle invasive or metastatic disease. Biomarkers for disease surveillance are urgently needed.

Objective: Development of assays for surveillance using genomic variants in cell-free tumour DNA from plasma and urine.

Design, setting, and participants: Retrospective pilot study of 377 samples from 12 patients with recurrent or progressive/metastatic disease. Three next-generation sequencing methods were applied and somatic variants in DNA from tumour, plasma, and urine were subsequently monitored by personalised assays using droplet digital polymerase chain reaction (ddPCR). Samples were collected from 1994 to 2015, with up to 20 yr of follow-up.

Outcome measurements and statistical analysis: Progression to muscle-invasive or metastatic bladder cancer; t test for ddPCR data.

Results and limitations: We developed from one to six personalised assays per patient. Patients with progressive disease showed significantly higher levels of tumour DNA in plasma and urine before disease progression, compared with patients with recurrent disease (p=0.032 and 1.3×10(-6), respectively). Interestingly, tumour DNA was detected in plasma and urine in patients with noninvasive disease, being no longer detectable in disease-free patients. A significant level of heterogeneity was observed for each patient; this could be due to tumour heterogeneity or assay performance.

Conclusions: Cell-free tumour DNA can be detected in plasma and urine, even in patients with noninvasive disease, with high levels of tumour DNA detectable before progression, especially in urine samples. Personalised assays of genomic variants may be useful for disease monitoring.

Patient summary: Tumour DNA can be detected in blood and urine in early and advanced stages of bladder cancer. Measurement of these highly tumour-specific biomarkers may represent a novel diagnostic tool to indicate the presence of residual disease or to discover aggressive forms of bladder cancer early in the disease course.

Keywords: Biomarker; Cell-free DNA; Circulating DNA; Droplet digital PCR; Genomic variant; NMIBC; Next-generation sequencing; Personalised analysis; Plasma; Urine.