The Utility of Mutations in Circulating Free DNA as Potential Predictive Biomarkers for Mechanism Based Therapeutics in Cancer Treatment

Abstract

Background Tumour specific somatic mutations can be detected in circulating free DNA (cfDNA) of patients with cancer. Lack of qualification hampers the routine use of cfDNA based assays in clinic. Next generation sequencing (NGS) of cfDNA may allow real time monitoring of genetic evolution in human cancers.Methods Analytical validation of BRAF c.1799T>A (p.V600E) mutation testing in cfDNA by allele specific real time PCR was performed using serum/plasma samples from 221 patients with advanced melanoma. Prognostic and predictive significance of cfDNA BRAF mutation detection was examined within the context of a MEK inhibitor trial in tumour BRAF mutant advanced melanoma. Targeted NGS of cfDNA was also performed in 8 patients with advanced colorectal cancer (CRC).Results Plasma contains higher proportion of tumour derived mutant DNA than serum. Using mutation calling criteria optimized for cfDNA improves sensitivity of BRAF c.1799T>A mutation detection by an allele specific PCR. cfDNA BRAF mutation status was an independent predictor of progression free survival in advanced melanoma patients with BRAF mutant tumours, of whom those with no mutation in cfDNA may derive better clinical benefits from MEK inhibition with selumetininb. In advanced CRC, cfDNA mutation profiling is complementary to tumour mutation profiling and FBXW7 mutation may play critical role in development of resistance to 5-Fluouracil based combination chemotherapies.Conclusions Plasma should be the clinical matrix of choice for cfDNA mutation testing. Biological significance of cfDNA mutation status should be studied and understood within specific clinical contexts before cfDNA based assays are clinically qualified. Targeted NGS of cfDNA could advance our understanding of treatment resistance mechanism in individual patients with cancer.

Date of Award	31 Dec 2014
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Caroline Dive (Supervisor) & Gerard Brady (Supervisor)