Detection of sarcoma fusions by a next-generation sequencing based–ligation-dependent multiplex RT-PCR assay

• DOI: 10.1038/s41379-021-00980-x
• Publication Date: 2022-01-24T05:02:37Z
• Authors: Marie-Delphine Lanic; François Le Loarer; Vinciane Rainville; Vincent Sater; Mathieu Viennot; Ludivine Beaussire; Pierre-Julien Via...; Emilie Angot; Isabelle Hostein; Fabrice Jardin; Philippe Ruminy; Marick Laé
• Keywords: 0301 basic medicine; Oncogene Proteins, Fusion; Reverse Transcriptase Polymerase Chain Reaction; [SDV]Life Sciences [q-bio]; High-Throughput Nucleotide Sequencing; Sarcoma; Soft Tissue Neoplasms; Endometrial Neoplasms; 3. Good health; [SDV] Life Sciences [q-bio]; 03 medical and health sciences; Formaldehyde; Humans; RNA; Female; In Situ Hybridization, Fluorescence

Morphological, immunohistochemical, and molecular methods often need to be combined for accurate diagnosis and optimal clinical management of sarcomas. Here, we have developed, a new molecular diagnostic assay, for the detection of gene fusions in sarcomas. This targeted multiplexed next-generation sequencing (NGS)-based method utilizes ligation dependent reverse-transcriptase polymerase chain reaction (LD-RT-PCR-NGS) to detect oncogenic fusion transcripts involving 137 genes, leading to 139 gene fusions known to be recurrently rearranged in soft-tissue and bone tumors. 158 bone and soft-tissue tumors with previously identified fusion genes by fluorescent in situ hybridization (FISH) or RT-PCR were selected to test the specificity and the sensitivity of this assay. RNA were extracted from formalin-fixed paraffin-embedded (n = 143) or frozen (n = 15) material (specimen; n = 42 or core needle biopsies; n = 116). Tested tumors encompassed 23 major translocation-related sarcomas types, including Ewing and Ewing-like sarcomas, rhabdomyosarcomas, desmoplastic small round-cell tumors, clear-cell sarcomas, infantile fibrosarcomas, endometrial stromal sarcomas, epithelioid hemangioendotheliomas, alveolar soft-part sarcomas, biphenotypic sinonasal sarcomas, extraskeletal myxoid chondrosarcomas, myxoid/round-cell liposarcomas, dermatofibrosarcomas protuberans and solitary fibrous tumors. In-frame fusion transcripts were detected in 98.1% of cases (155/158). Gene fusion assay results correlated with conventional techniques (FISH and RT-PCR) in 155/158 tumors (98.1%). These data demonstrate that this assay is a rapid, robust, highly sensitive, and multiplexed targeted RNA sequencing assay for the detection of recurrent gene fusions on RNA extracted from routine clinical specimens of sarcomas (formalin-fixed paraffin-embedded or frozen). It facilitates the precise diagnosis and identification of tumors with potential targetable fusions. In addition, this assay can be easily customized to cover new fusions.