Performance of the permutation test approach with base calling errors for detecting changes in variant allele frequencies in ctDNA for a single patient

Serial measurements of circulating tumor DNA (ctDNA) with next-generation sequencing (NGS) technology enable the real-time, noninvasive evaluation of longitudinal changes of molecular profiles in tumor tissues. These profiles can assist in monitoring disease progression and tumor response to targeted therapies, thereby facilitating informed therapeutic decision making through precise molecular characterization. While base calling errors are inherent in detecting ctDNA mutations, there is limited consideration of the effect of base calling errors on detecting variant allele frequency (VAF) changes. This study introduces the likelihood functions that incorporate the base calling error probabilities and proposes the permutation test for detecting VAF changes between two time points for a patient. Simulation studies, with scenarios based on real NGS analysis data from the TOP-GEAR project, showed that the proposed test maintained the nominal significance level at two-sided 0.05 regardless of the base calling error probabilities and VAFs. In our scenarios with 500 depth at each time point, the power of 80 % was achievable for a twofold or more increase when the VAF was 0.05 at baseline and a half or more decrease when the VAF was 0.1. Our empirical results show the utility and potential of the permutation test to detect VAF changes.