Feasibility of a novel non-invasive swab technique for serial whole-exome sequencing of cervical tumors during chemoradiation therapy

Abstract

Background: Clinically relevant genetic predictors of radiation response for cervical cancer are understudied due to the morbidity of repeat invasive biopsies required to obtain genetic material. Thus, we aimed to develop a novel noninvasive cervical swab technique to collect tumor DNA with adequate throughput to perform whole-exome sequencing (WES) at serial time points over the course of chemoradiation therapy (CRT). Methods: Cervical cancer tumor samples from patients undergoing chemoradiation were collected at baseline, at week 1, week three, and at the completion of CRT (week 5) using a noninvasive swab-based biopsy technique. Swab samples were analyzed with whole-exome sequencing (WES) with mutation calling using a custom pipeline optimized for shallow whole-exome sequencing with low tumor purity. Tumor mutation changes over the course of treatment were profiled. Results: 217 samples were collected and successfully sequenced for 70 patients. A total of 33 patients had a complete set of samples at all four time points. The mean mapping rate was 98% for all samples, and the mean target coverage was 180. Overall mutation frequency decreased during CRT with disease response but mapping rate and mean target coverage remained at >98% and >180 reads at week 5. Conclusion: This study demonstrates the feasibility and application of a noninvasive swab-based technique for WES analysis to investigate dynamic tumor mutational changes during treatment and may be a valuable approach to identify novel genes which confer radiation resistance.