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Detection of low frequency FGFR3 mutations in the urine of bladder cancer patients using next-generation deep sequencing
Authors Millholland, Li, Fernandez C, Shuber A
Received 7 April 2012
Accepted for publication 18 May 2012
Published 27 June 2012 Volume 2012:4 Pages 33—40
DOI https://doi.org/10.2147/RRU.S32736
Review by Single anonymous peer review
Peer reviewer comments 2
John M Millholland, Shuqiang Li, Cecilia A Fernandez, Anthony P Shuber
Predictive Biosciences Inc, Lexington, MA, USA
Abstract: Biological fluid-based noninvasive biomarker assays for monitoring and diagnosing disease are clinically powerful. A major technical hurdle for developing these assays is the requirement of high analytical sensitivity so that biomarkers present at very low levels can be consistently detected. In the case of biological fluid-based cancer diagnostic assays, sensitivities similar to those of tissue-based assays are difficult to achieve with DNA markers due to the high abundance of normal DNA background present in the sample. Here we describe a new urine-based assay that uses ultradeep sequencing technology to detect single mutant molecules of fibroblast growth factor receptor 3 (FGFR3) DNA that are indicative of bladder cancer. Detection of FGFR3 mutations in urine would provide clinicians with a noninvasive means of diagnosing early-stage bladder cancer. The single-molecule assay detects FGFR3 mutant DNA when present at as low as 0.02% of total urine DNA and results in 91% concordance with the frequency that FGFR3 mutations are detected in bladder cancer tumors, significantly improving diagnostic performance. To our knowledge, this is the first practical application of next-generation sequencing technology for noninvasive cancer diagnostics.
Keywords: FGFR3, mutation, urine, single molecule, sequencing, bladder cancer
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