Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas

Abstract

Background: Synovial sarcoma (SS) is a malignant soft tissue tumor of mesenchymal origin that frequently occurs in young adults. Translocation of the SYT gene on chromosome 18 to the SSX genes on chromosome X leads to the formation of oncogenic fusion genes, which lead to initiation and proliferation of tumor cells. The detection and quantification of circulating tumor DNA (ctDNA) can serve as a non-invasive method for diagnostics of local or distant tumor recurrence, which could improve survival rates due to early detection. Methods: We developed a subtype-specific targeted next-generation sequencing (NGS) approach specifically targeting SS t(X;18)(p11;q11), which fuses SS18 (SYT) in chromosome 18 to SSX1 or SSX2 in chromosome x, and recurrent point mutations. In addition, patient-specific panels were designed from tumor exome sequencing. Both approaches were used to quantify ctDNA in patients’ plasma. Results: The subtype-specific assay allowed detection of somatic mutations from 25/25 tumors with a mean of 1.68 targetable mutations. The minimal limit of detection was determined at a variant allele frequency of 0.05%. Analysis of 29 plasma samples from 15 tumor patients identified breakpoint ctDNA in 6 patients (sensitivity: 40%, specificity 100%). The addition of more mutations further increased assay sensitivity. Quantification of ctDNA in plasma samples (n = 11) from one patient collected over 3 years, with a patient-specific panel based on tumor exome sequencing, correlated with the clinical course, response to treatment and tumor volume. Conclusions: Targeted NGS allows for highly sensitive tumor profiling and non-invasive detection of ctDNA in SS patients, enabling non-invasive monitoring of tumor dynamics.

Outcomes After Preoperative Chemoradiation With or Without Pazopanib in Non-Rhabdomyosarcoma Soft Tissue Sarcoma: A Report From Children's Oncology Group and NRG Oncology

“…Less invasive diagnostic techniques such as fluorodeoxyglucose positron emission tomography and circulating tumor DNA are particularly appealing and are actively being evaluated in this setting. 14,15 Within the statistical limitations of our analysis, however, pathologic response cannot be considered a surrogate marker of response and predictor of outcome in pediatric and adult patients with extremity and trunk soft tissue sarcoma treated with neoadjuvant chemoradiotherapy and pazopanib.…”

Soft Tissue Sarcomas in Adolescents and Young Adults

“…56 Such opportunities exist across a spectrum of disciplines including pathology (eg, pathologic response), imaging (positron emission tomography, T2 magnetic resonance imaging), and biology (eg, methylation, proteomics, circulating tumor DNA). [57][58][59][60][61][62] Currently, these efforts have largely analyzed pediatric and adult patients separately, preventing an opportunity to determine their prognostic significance across the AYA population.…”

Non-invasive monitoring of neoadjuvant radiation therapy response in soft tissue sarcomas by multiparametric MRI and quantification of circulating tumor DNA—A study protocol

“…Subtype-specific panel sequencing for myxoid liposarcomas and synovial sarcomas [33,34]. DNA from tumor tissue (native or FFPE) and matched controls from whole blood samples are prepared for sequencing by generating libraries using NEB kit NEBNext Ultra II FS DNA Library Prep Kit for Illumina, (New England Biolabs, Ipswich, USA).…”

“…Quantification of ctDNA in the peripheral circulation might even surpass common imaging modalities in its sensitivity and specificity to detect tumors or metastases [26][27][28]. In previous works, the Department of Plastic and Hand Surgery, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany, has shown that liquid biopsy can be used to monitor tumor dynamics, predict minimal residual disease and detect genetic tumor heterogeneities [3,[28][29][30][31][32][33][34]. The question remains, whether ctDNA can also be used as a biomarker for tumor activity.…”