Whole-genome optical mapping for comprehensive analysis of sarcoma genomes in a diagnostic setting

Over the past few decades, several innovative molecular techniques have been introduced in clinical oncology practice. One of these tools is short-read next generation sequencing (NGS), a technique that led to a significant improvement in cancer diagnosis and treatment due to the identification of targetable driver mutations and/or gene fusions. However, NGS has mainly revolutionized clinical practice in common epithelial cancer types but remains unsatisfactory when applied to rare tumor types such as malignant soft tissue and bone tumors. These tumors, also called sarcomas, represent less than 2% of solid tumors with 1181 new diagnoses in Belgium in 2018 [1]. Sarcomas are highly heterogeneous in terms of histological presentation (> 100 subtypes to date), clinical disease course and underlying genetic aberrations. Accurate determination of genetic aberrations significantly adds to a correct diagnosis, which is strongly associated with patient treatment. However, genetic testing of sarcomas is not straight-forward today. Indeed, while some sarcoma subtypes carry a characteristic gene mutation or fusion, many remain poorly characterized or show multiple, complex genetic aberrations caused by chromothripsis or catastrophic chromosomal breakage [2,3]. These complex aberrations are difficult to detect by short-read NGS and typically include structural variants in which larger DNA segments undergo chromosomal perturbations such as translocations, deletions, duplications, insertions or inversions. Therefore, a combination of several cytogenetic techniques is currently required for the diagnostic workup of sarcomas including conventional karyotyping, array Comparative Genomic Hybridization (aCGH), and Fluorescent In Situ Hybridization (FISH), next to short-read NGS. This combined approach is needed because standard cytogenetic techniques have several shortcomings including limited resolution (karyotyping) or the inability to detect certain structural variants like balanced translocations (aCGH). As a result, genetic testing of sarcomas is labor-intensive, costly and requires a substantial amount of tumor tissue which is not always available. With this project, we aim to implement a novel technology called Optical Genomic Mapping (OGM). OGM is a non-sequencing based technology that allows genome-wide detection of structural variants and copy number alterations, and therefore has the potential to replace the above-mentioned standard cytogenetic techniques by one single test, as recently demonstrated by Neveling et al for hematological malignancies [4,5]. As compared to long-read sequencing methods such as PacBio or Nanopore, OGM has the advantage that it does not suffer from sequencing errors. Implementing OGM for sarcoma diagnostics will lead to more comprehensive and cost-effective genetic analysis, rapidly revealing structural variants and copy number variation in patient samples. This novel approach will not only result in improved diagnosis but may also reveal novel driver events in poorly characterized sarcomas.