Abstract 2288: Identification of gene fusions in soft tissue sarcoma improved by integrative DNA and RNA sequencing

Abstract

Abstract Background: More than 50 different histologic subtypes of soft tissue sarcoma (STS) with mesenchymal origin have been recognized, and their overlapping morphology and histology make clinical diagnosis challenging. Gene fusion has been described as an important molecular biological feature of STS, which can assist in its diagnosis and treatment. Conventional DNAseq methods have limitations for gene fusion detection, while the RNAseq method might circumvent them. In this study, we evaluated the clinical value of integrated DNA and RNA sequencing in the detection of STS gene fusions. Methods: Formalin-fixed and paraffin embedded (FFPE) tumor samples and matched blood of 142 Chinese STS patients were collected and tested by the next-generation sequencing (NGS)-based 825-gene DNA panel and 395-gene RNA panel at Genetronhealth, a laboratory accredited by College of American Pathologists and Clinical Laboratory Improvement Amendments. Results: The genetic landscape of 75 male and 67 female Chinese patients with STS was analyzed. The median age of enrolled patients was 39 years (range, 1-82 years). Multiple histological subtypes were collected, including rhabdomyosarcoma (n = 15), liposarcoma (n = 15), myofibroblastic sarcoma (n = 11) and other types which were all less than 10 cases. Overall, 83 different fusions were detected in 60 patients. Of these, 25 fusions could be detected both by DNA and RNA panels in 18 patients, five fusions were detected only by the DNA panel in four patients, and 53 fusions only by the RNA panel in 39 patients. Compared to DNA-NGS individual testing, integrative panels increased the detection rate of fusion in patients with STS by 177% (53/30). The five gene fusions detected only by the DNA panel, including FOSL1-RELA, intergenic-RUNX2, ADAMTS16-TERT, NCR3LG1-KMT2A and YAP1-MAMLD1, remain clinical significance uncertain in STS. Fusion genes, such as PAX3-FOXO1, ASPSCR1-TFE3, COL1A1-PDGFB, EWSR1-ERG, were detected separately by the RNA panel, which could assist the diagnosis or targeted therapy. Additionally, unreported DIP2B-EWSR1 and AMLD1-SSX1 gene fusions were detected in a patient with clear cell sarcoma and a patient with synovial sarcoma respectively, which might be helpful in clinical diagnosis. Conclusions: Our results showed that the integrated DNA and RNA sequencing can effectively improve the detection rate of STS gene fusions, which might benefit more STS patients. Citation Format: Jiayong Liu, Shu Li, Tian Gao, Chunyang Wang, Qifan He, Xiaojuan Wang, Tonghui Ma. Identification of gene fusions in soft tissue sarcoma improved by integrative DNA and RNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2288.