Patient-specific sequencing panels enable sensitive circulating tumor DNA analysis in rhabdomyosarcoma independent of genetic profile

No liquid biomarkers are available for monitoring rhabdomyosarcoma, and treatment evaluation is limited to imaging examinations. Circulating tumor DNA (ctDNA) is a promising disease marker in various malignancies, but generalized ctDNA assays targeting recurrent mutations are unsuitable for childhood sarcomas due to genetic heterogeneity. We developed tumor-informed sequencing panels targeting ten single-nucleotide variants per patient and performed ultrasensitive ctDNA analysis of 130 plasma samples in twelve children with rhabdomyosarcoma. Levels of ctDNA correlated with tumor burden, decreased gradually and became undetectable with successful treatment. All four disease relapses and the one case of primary resistant disease were associated with increased ctDNA levels. In one patient, ctDNA was repeatedly positive during five months before clinical relapse. In contrast, all samples collected during follow-up in patients without relapse were ctDNA-negative. Our findings show that ctDNA, analyzed using a tumor-informed approach, is a sensitive and specific biomarker for rhabdomyosarcoma, also for patients lacking recurrent genetic alterations.