Individualized Mini-Panel Sequencing of ctDNA Allows Tumor Monitoring in Complex Karyotype Sarcomas

Abstract

Soft tissue sarcomas (STS) are rare tumors of mesenchymal origin with high mortality. After curative resection, about one third of patients suffer from distant metastases. Tumor follow-up only covers a portion of recurrences and is associated with high cost and radiation burden. For metastasized STS, only limited inferences can be drawn from imaging data regarding therapy response. To date there are no established and evidence-based diagnostic biomarkers for STS due to their rarity and diversity. In a proof-of-concept study, circulating tumor DNA (ctDNA) was quantified in (n = 25) plasma samples obtained from (n = 3) patients with complex karyotype STS collected over three years. Genotyping of tumor tissue was performed by exome sequencing. Patient-individual mini-panels for targeted next-generation sequencing were designed encompassing up to 30 mutated regions of interest. Circulating free DNA (cfDNA) was purified from plasma and ctDNA quantified therein. ctDNA values were correlated with clinical parameters. ctDNA concentrations correlated with the tumor burden. In case of full remission, no ctDNA was detectable. Patients with a recurrence at a later stage showed low levels of ctDNA during clinical remission, indicating minimal residual disease. In active disease (primary tumor or metastatic disease), ctDNA was highly elevated. We observed direct response to treatment, with a ctDNA decline after tumor resections, radiotherapy, and chemotherapy. Quantification of ctDNA allows for the early detection of recurrence or metastases and can be used to monitor treatment response in STS. Therapeutic decisions can be made earlier, such as the continuation of a targeted adjuvant therapy or the implementation of extended imaging to detect recurrences. In metastatic disease, therapy can be adjusted promptly in case of no response. These advantages may lead to a survival benefit for patients in the future.

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

“…In the literature [24,58,59] and previous works by our group [28][29][30][31][32][33][34]45], ctDNA is described as a potential biomarker for the prediction of STS, its recurrence, and minimal residual disease PLOS ONE after resection. However, it has not been shown if ctDNA can be used as a biomarker for therapy response and how ctDNA correlates with vital tumor mass during NRT.…”

“…Targeted sequencing of ctDNA improves STS detection independent of its anatomic localization and can be performed anytime during the course of treatment. 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].…”

“…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.…”