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Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours.
Zago Baltazar, Rafael; Claerhout, Sofie; Vander Borght, Sara; Spans, Lien; Sciot, Raphael; Schöffski, Patrick; Hompes, Daphne; Sinnaeve, Friedl; Wafa, Hazem; Renard, Marleen; van den Hout, Mari Fcm; Vernemmen, Astrid; Libbrecht, Louis; De Roo, An-Katrien; Mazzeo, Filomena; van Marcke, Cédric; Deraedt, Karen; Bourgain, Claire; Vanden Bempt, Isabelle.
Afiliación
  • Zago Baltazar R; Department of Human Genetics, University Hospitals KU Leuven, Leuven, Belgium.
  • Claerhout S; Department of Human Genetics, University Hospitals KU Leuven, Leuven, Belgium.
  • Vander Borght S; Department of Human Genetics, University Hospitals KU Leuven, Leuven, Belgium.
  • Spans L; Department of Pathology, University Hospitals KU Leuven, Leuven, Belgium.
  • Sciot R; Department of Human Genetics, University Hospitals KU Leuven, Leuven, Belgium.
  • Schöffski P; Department of Pathology, University Hospitals KU Leuven, Leuven, Belgium.
  • Hompes D; Department of General Medical Oncology, University Hospitals KU Leuven, Leuven, Belgium.
  • Sinnaeve F; Department of Surgical Oncology, University Hospitals KU Leuven, Leuven, Belgium.
  • Wafa H; Department of Orthopaedic Surgery, University Hospitals KU Leuven, Leuven, Belgium.
  • Renard M; Department of Orthopaedic Surgery, University Hospitals KU Leuven, Leuven, Belgium.
  • van den Hout MF; Department of Paediatric Hemato-Oncology, University Hospitals KU Leuven, Leuven, Belgium.
  • Vernemmen A; Department of Pathology, Maastricht University Medical Center+, Maastricht, The Netherlands.
  • Libbrecht L; Department of Pathology, Maastricht University Medical Center+, Maastricht, The Netherlands.
  • De Roo AK; Department of Pathology, Cliniques Universitaires Saint-Luc, Brussels, Belgium.
  • Mazzeo F; Department of Pathology, AZ Groeninge, Kortrijk, Belgium.
  • van Marcke C; Department of Pathology, Cliniques Universitaires Saint-Luc, Brussels, Belgium.
  • Deraedt K; Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium.
  • Bourgain C; Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium.
  • Vanden Bempt I; Breast Clinic, King Albert II Cancer Institute, Cliniques Universitaires Saint-Luc, Brussels, Belgium.
J Pathol Clin Res ; 10(3): e12376, 2024 May.
Article en En | MEDLINE | ID: mdl-38738521
ABSTRACT
The identification of gene fusions has become an integral part of soft tissue and bone tumour diagnosis. We investigated the added value of targeted RNA-based sequencing (targeted RNA-seq, Archer FusionPlex) to our current molecular diagnostic workflow of these tumours, which is based on fluorescence in situ hybridisation (FISH) for the detection of gene fusions using 25 probes. In a series of 131 diagnostic samples targeted RNA-seq identified a gene fusion, BCOR internal tandem duplication or ALK deletion in 47 cases (35.9%). For 74 cases, encompassing 137 FISH analyses, concordance between FISH and targeted RNA-seq was evaluated. A positive or negative FISH result was confirmed by targeted RNA-seq in 27 out of 49 (55.1%) and 81 out of 88 (92.0%) analyses, respectively. While negative concordance was high, targeted RNA-seq identified a canonical gene fusion in seven cases despite a negative FISH result. The 22 discordant FISH-positive analyses showed a lower percentage of rearrangement-positive nuclei (range 15-41%) compared to the concordant FISH-positive analyses (>41% of nuclei in 88.9% of cases). Six FISH analyses (in four cases) were finally considered false positive based on histological and targeted RNA-seq findings. For the EWSR1 FISH probe, we observed a gene-dependent disparity (p = 0.0020), with 8 out of 35 cases showing a discordance between FISH and targeted RNA-seq (22.9%). This study demonstrates an added value of targeted RNA-seq to our current diagnostic workflow of soft tissue and bone tumours in 19 out of 131 cases (14.5%), which we categorised as altered diagnosis (3 cases), added precision (6 cases), or augmented spectrum (10 cases). In the latter subgroup, four novel fusion transcripts were found for which the clinical relevance remains unclear NAB2NCOA2, YAP1NUTM2B, HSPA8BRAF, and PDE2APLAG1. Overall, targeted RNA-seq has proven extremely valuable in the diagnostic workflow of soft tissue and bone tumours.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias de los Tejidos Blandos / Neoplasias Óseas / Hibridación Fluorescente in Situ / Flujo de Trabajo Límite: Adolescent / Adult / Aged / Aged80 / Child / Child, preschool / Female / Humans / Male / Middle aged Idioma: En Revista: J Pathol Clin Res Año: 2024 Tipo del documento: Article País de afiliación: Bélgica Pais de publicación: Reino Unido
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Neoplasias de los Tejidos Blandos / Neoplasias Óseas / Hibridación Fluorescente in Situ / Flujo de Trabajo Límite: Adolescent / Adult / Aged / Aged80 / Child / Child, preschool / Female / Humans / Male / Middle aged Idioma: En Revista: J Pathol Clin Res Año: 2024 Tipo del documento: Article País de afiliación: Bélgica Pais de publicación: Reino Unido