In a study from the Children’s Oncology Group reported in the Journal of Clinical Oncology, Abbou et al found that measuring circulating tumor DNA (ctDNA) in intermediate-risk rhabdomyosarcoma was feasible and that the presence of ctDNA prior to treatment was associated with poorer prognosis.
As stated by the investigators, “Novel biomarkers are needed to differentiate outcomes in intermediate-risk rhabdomyosarcoma. We sought to evaluate strategies for identifying ctDNA in intermediate-risk rhabdomyosarcoma and to determine whether ctDNA detection before therapy is associated with outcome.”
Study Details
The study used pretreatment serum and tumor samples from 124 patients with newly diagnosed intermediate-risk rhabdomyosarcoma from the Children’s Oncology Group biorepository, including 75 with fusion-negative rhabdomyosarcoma (FN-RMS) and 49 with fusion-positive rhabdomyosarcoma (FP-RMS). As noted by the investigators, FP-RMS and FN-RMS represent the two genetic subtypes of rhabdomyosarcoma: FP-RMS is characterized by somatic translocation between FOXO1 and either PAX3 or PAX7; FN-RMS is characterized by aneuploidy and recurrent single-nucleotide variants, often in RAS pathway genes.
Ultralow passage whole-genome sequencing was used to detect copy number alterations. To identify translocations and single-nucleotide variants, the investigators designed a rhabdomyosarcoma-specific hybrid capture assay—Rhabdo-Seq—to target intronic regions of FOXO1, PAX3, PAX7, VGLL2, CITED2, NCOA1, and NCOA2 to detect translocations and to target coding regions of 24 genes recurrently mutated in rhabdomyosarcoma.
Key Findings
Ultralow passage whole-genome sequencing was found to be a method applicable to ctDNA detection in all patients with FN-RMS; pretreatment ctDNA was detectable in 13 (17%) of 75 serum samples.
Use of the Rhabdo-Seq assay in FN-RMS samples also identified single-nucleotide variants previously associated with prognosis. Identification of translocations between PAX3 or PAX7 and FOXO1 by Rhabdo-Seq was the best method for measuring ctDNA in FP-RMS, with pretreatment ctDNA identified in 27 (55%) of 49 cases.
Among patients with FN-RMS, detectable vs no detectable ctDNA at diagnosis was associated with significantly worse 5-year event-free survival (33.3% vs 68.9%, P = .0028) and overall survival (33.3% vs 83.2%, P < .0001). Among patients with FP-RMS, detectable vs no detectable ctDNA at diagnosis was associated with significantly poorer 5-year event-free survival (37% vs 70%, P = .045) and overall survival (39.2% vs 75%, P = .023).
In multivariate analysis in the FN-RMS cohort, hazard ratios for the presence of ctDNA were 4.0 (95% CI = 1.7–9.4, P = .0016) for event-free survival and 6.5 (95% CI = 2.5–16.6, P < .0001) for overall survival. In multivariate analysis in the FP-RMS cohort, hazard ratios for the presence of ctDNA were 2.5 (95% CI = 1.0–6.4, P = .05) for event-free survival and 3.1 (95% CI = 1.1–8.4, P = .03) for overall survival. Among 25 patients with copy number alterations, ctDNA detection by ultralow passage whole-genome sequencing was not significantly associated with outcomes.
The investigators concluded, “Our study demonstrates that baseline ctDNA detection is feasible and is prognostic in intermediate-risk rhabdomyosarcoma.”
Brian D. Crompton, MD, of Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, is the corresponding author for the Journal of Clinical Oncology article.
Disclosure: The study was supported by the Children’s Oncology Group Translational Pilot Studies Program for Solid Malignancies, National Cancer Institute grants, St. Baldrick’s Foundation, and others. For full disclosures of the study authors, visit ascopubs.org.
