Performance of the permutation test approach with base calling errors for detecting changes in variant allele frequencies in ctDNA for a single patient
Randomized trial evaluates a new test for monitoring variant allele frequency changes in ctDNA, suggesting improved disease tracking.
Key Points
This research aims to evaluate the performance of a permutation test for detecting changes in variant allele frequencies (VAFs) in circulating tumor DNA (ctDNA) considering base calling errors.
Introduced likelihood functions accounting for base calling error probabilities.
Employed a permutation test to assess VAF changes between two time points for one patient.
Conducted simulation studies based on realistic NGS analysis data from the TOP-GEAR project.
Test maintained nominal significance level of 0.05 regardless of error probabilities and VAFs.
Achieved 80% power for detecting a twofold increase in VAF starting from 0.05 at baseline.
Demonstrated capability to detect a half or more decrease from a baseline VAF of 0.1.