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© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

Sarcomas are rare malignant tumors of mesenchymal origin with a high misdiagnosis rate due to their heterogeneity and low incidence. Conventional diagnostic techniques, such as Fluorescence In Situ Hybridization (FISH) and Next-Generation Sequencing (NGS), have limitations in detecting structural variations (SVs), copy number variations (CNVs), and predicting clinical behavior. Optical genome mapping (OGM) provides high-resolution genome-wide analysis, improving sarcoma diagnosis and prognosis assessment. This study analyzed 53 sarcoma samples using OGM. Ultra-high molecular weight (UHMW) DNA was extracted from core and resection biopsies, and data acquisition was performed with the Bionano Saphyr platform. Bioinformatic pipelines identified structural variations, comparing them with known alterations for each sarcoma subtype. OGM successfully analyzed 62.3% of samples. Diagnostic-defining alterations were found in 95.2% of cases, refining diagnoses and revealing novel oncogenic and tumor suppressor gene alterations. The challenges included DNA extraction and quality issues from some tissue samples. Despite these limitations, OGM proved to be a powerful diagnostic and predictive tool for bone and soft tissue sarcomas, surpassing conventional methods in resolution and scope, enhancing the understanding of sarcoma genetics, and enabling better patient stratification and personalized therapies.

Details

Title
Exploring the Potential of Optical Genome Mapping in the Diagnosis and Prognosis of Soft Tissue and Bone Tumors
Author
Berenguer-Rubio, Alejandro 1   VIAFID ORCID Logo  ; Such, Esperanza 2   VIAFID ORCID Logo  ; Neus Torres Hernández 1   VIAFID ORCID Logo  ; González-Rojo, Paula 3   VIAFID ORCID Logo  ; Díaz-González, Álvaro 1 ; Avetisyan, Gayane 1 ; Gil-Aparicio, Carolina 1 ; González-López, Judith 3   VIAFID ORCID Logo  ; Pantoja-Borja, Nicolay 3 ; Rubio-Martínez, Luis Alberto 3 ; Hernández-Girón, Soraya 3 ; Valera-Cuesta, María Soledad 3 ; Ramírez-Fuentes, Cristina 4 ; Simonet-Redondo, María 4 ; Díaz-Beveridge, Roberto 5 ; de la Calva, Carolina 6 ; José Vicente Amaya-Valero 6 ; Ballester-Ibáñez, Cristina 7 ; Liquori, Alessandro 8 ; Giner, Francisco 3 ; Mayordomo-Aranda, Empar 3 

 Cytogenetic Laboratory, Instituto de Investigación Sanitaria La Fe, 46026 València, Spain; [email protected] (A.B.-R.); [email protected] (N.T.H.); [email protected] (Á.D.-G.); [email protected] (G.A.); [email protected] (C.G.-A.); Department of Hematology, Hospital Universitari i Politècnic La Fe, 46026 València, Spain; [email protected] 
 Cytogenetic Laboratory, Instituto de Investigación Sanitaria La Fe, 46026 València, Spain; [email protected] (A.B.-R.); [email protected] (N.T.H.); [email protected] (Á.D.-G.); [email protected] (G.A.); [email protected] (C.G.-A.); Department of Hematology, Hospital Universitari i Politècnic La Fe, 46026 València, Spain; [email protected]; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain 
 Pathology Department, Hospital Universitari i Politècnic La Fe, 46026 València, Spain; [email protected] (P.G.-R.); [email protected] (J.G.-L.); [email protected] (N.P.-B.); [email protected] (L.A.R.-M.); [email protected] (S.H.-G.); [email protected] (M.S.V.-C.); [email protected] (F.G.); [email protected] (E.M.-A.) 
 Radiology Department, Hospital Universitari i Politècnic La Fe, 46026 València, Spain; [email protected] (C.R.-F.); [email protected] (M.S.-R.) 
 Medical Oncology Service, Hospital Universitari i Politècnic La Fe, 46026 València, Spain; [email protected] 
 Orthopaedics and Traumatology Department, Hospital Universitari i Politècnic La Fe, 46026 València, Spain; [email protected] (C.d.l.C.); [email protected] (J.V.A.-V.) 
 Department of Orthopaedic Surgery, Hospital Universitari i Politècnic La Fe, 46026 València, Spain; [email protected] 
 Department of Hematology, Hospital Universitari i Politècnic La Fe, 46026 València, Spain; [email protected] 
First page
2820
Publication year
2025
Publication date
2025
Publisher
MDPI AG
ISSN
16616596
e-ISSN
14220067
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
3181485487
Copyright
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.