Whole Genome Sequencing and Custom Liquid Biopsy Markers in Sarcomas

Abstract

Background: Sarcomas are rare tumours with heterogeneous clinical behaviour including varying rates of metastasis. Clinical treatment and follow-up rely on crude grading systems with uncertain accuracy for individual patients. Whole genome sequencing (WGS) detects both structural variation and single nucleotide variants and may thus add important diagnostic/prognostic information. Liquid biopsies (LB) may potentially identify hematogenous spread and treatment response rate but further evaluation in sarcomas is needed. Methods: In this study we explore the performance of individualized LB in four patients with different types of sarcomas. Fresh frozen tumour tissue was sequenced using WGS and whole transcriptome sequencing. Three putative driver variants or one fusion gene were selected per case and custom digital droplet PCR (ddPCR) assays were designed, evaluated on tumour DNA and used to assess levels of cell free tumour DNA in plasma taken prior to surgery. Results: In LB, ddPCR identified three variants in one patient with metastatic disease. The remaining three patients had negative LBs and were without disease at follow-up (>18 months after surgery). Conclusions: WGS is a powerful tool to detect all types of genetic changes in sarcoma and can facilitate clinical diagnosis/classification while custom LB may add prognostic information.