Detection of circulating tumor DNA in patients with osteosarcoma

Abstract

Identification and quantification of somatic alterations in plasma-derived, circulating tumor DNA (ctDNA) is gaining traction as a non-invasive and cost effective method of disease monitoring in cancer patients, particularly to evaluate response to treatment and monitor for disease recurrence. To our knowledge, genetic analysis of ctDNA in osteosarcoma has not yet been studied. To determine whether somatic alterations can be detected in ctDNA and perhaps applied to patient management in this disease, we collected germline, tumor, and serial plasma samples from pediatric, adolescent, and young adult patients with osteosarcoma and used targeted Next Generation Sequencing (NGS) to identify somatic single nucleotide variants (SNV), insertions and deletions (INDELS), and structural variants (SV) in 7 genes commonly mutated in osteosarcoma. We demonstrate that patient-specific somatic alterations identified through comparison of tumor-germline pairs can be detected and quantified in cell-free DNA of osteosarcoma patients.

Keywords: Next Generation Sequencing; circulating tumor DNA; osteosarcoma; targeted sequencing; targeted therapy.

Figure 1. Clinical time points of plasma samples that underwent genomic analysis

Figure 2. Abundance of structural alteration with associated clinical course

Each sample collection is represented by large square. Dotted lines serve to visually connect time points rather than represent individual collections. (A) The relative quantity of a translocation (TP53) in serially collected plasma samples. The first sample was drawn following the removal of lung nodules and initiation of treatment. Over the course of the study, the patient was diagnosed with disease relapse to the spine, and underwent surgical removal of the spine metastases. (B) The relative quantity of two SNVs, (chr X position 77033528 ATRX gene and chr 11 position 84514691 in DLG2 gene) in serially collected plasma samples. Samples were drawn during treatment of clinically progressive disease, after surgery on the primary tumor, and following discovery of metastases to the lung. (C) The relative quantity of an SNV, (chr 7 position 116427288 in MET gene) in serially collected plasma samples. Samples were drawn after completion of treatment of primary tumor as well as before and after surgical removal of a lung nodule. (D) The relative quantity of a TP53 intron 1 translocation in serially collected plasma samples. The translocation was discovered without matched tumor DNA. Samples were drawn after completion of primary treatment and during clinical progression of disease.