Individualized cell-free DNA monitoring with chromosomal junctions for mesothelioma

Introduction The spatially complex nature of mesothelioma and interventions like pleurodesis, surgery and radiation often complicate imaging-based assessment. Further, cell-free DNA (cfDNA) based monitoring strategies are inadequate for mesothelioma, given the presence of few recurring nonsynonymous somatic variants. However, patient specific chromosomal rearrangements are commonly found in mesothelioma. Our study objective was to develop an individualized cfDNA assay to enable blood-based monitoring using circulating tumor DNA (ctDNA) in mesothelioma. We hypothesized that the unique chromosomal rearrangement junctions found in mesothelioma could be employed for individualized ctDNA detection and disease monitoring. Methods DNA was extracted from tumor specimens for whole genome sequencing. Chromosomal junctions, prioritized by highest allele frequency and low homology to rest of the genome, were selected for detection. Primers and Taqman probes were designed to span the junctions, forming personalized junction panels. Patient plasma obtained prior to therapy and at response assessment was tested for the presence of personalized junctions via qPCR. Results Our study included nine patients, four with peritoneal and five with pleural mesothelioma. 763 chromosomal junctions were identified in the tumors of all cases. We selected three to five junctions per sample for qPCR. We detected 25/30 (83%) of selected junctions in plasma of 7 out of 9 patients (78%). Cell-free junction detection at follow-up was concordant with disease status: cfDNA junctions were detected in 3 patients with persistent disease, and not detected in a patient with no evidence of disease after surgery. Conclusion With further validation, individualized ctDNA junction assays could supplement imaging for disease monitoring in mesothelioma.