Optical Genome Mapping for Comprehensive Cytogenetic Analysis of Soft-Tissue and Bone Tumors for Diagnostic Purposes

Abstract

Soft tissue and bone tumours represent a heterogeneous group of tumours encompassing more than 100 histological subtypes today. Identifying genetic aberrations is increasingly important in these tumours for accurate diagnosis. While gene mutations are typically detected by second generation sequencing, the identification of structural variants (SVs) and copy number alterations (CNAs) remains challenging and requires various cytogenetic techniques including karyotyping, fluorescent in situ hybridisation and arrays, each having important limitations.We applied Optical Genome Mapping (OGM), a non-sequencing-based technique for high-resolution detection of SVs and CNAs in a retrospective series of diagnostic soft tissue and bone tumour samples. Sample preparation was successful in 38 out of 53 cases, with the highest success rate in non-adipocytic soft tissue tumours (24/27 cases, 89%). In 32 out of 35 cases carrying a diagnostic SV or CNA, OGM identified the aberration (91%) including a POU2AF3::EWSR1 fusion in a round cell sarcoma and a translocation t(1;5)(p22;p15) in a myxoinflammatory fibroblastic sarcoma. Interestingly, OGM shed light on the genomic complexity underlying the various aberrations. In five samples OGM showed that chains of rearrangements generated the diagnostic fusion, three of which involved chromoplexy. Additionally, in nine samples chromothripsis was causal to the formation of giant marker/ring/double minute chromosomes. Finally, compared to standard-of-care cytogenetics, OGM revealed additional aberrations, requiring further investigation of their potential clinical relevance.