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Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience

Accurate diagnoses of sarcoma are sometimes challenging on conventional histomorphology and immunophenotype. Many specific genetic aberrations including chromosomal translocations have been identified in various sarcomas, which can be detected by fluorescence in situ hybridization and polymerase cha...

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Autores principales: Pei, Jianming, Zhao, Xiaofeng, Patchefsky, Arthur S., Flieder, Douglas B., Talarchek, Jacqueline N., Testa, Joseph R., Wei, Shuanzeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Wolters Kluwer Health 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636967/
https://www.ncbi.nlm.nih.gov/pubmed/31232935
http://dx.doi.org/10.1097/MD.0000000000016031
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author Pei, Jianming
Zhao, Xiaofeng
Patchefsky, Arthur S.
Flieder, Douglas B.
Talarchek, Jacqueline N.
Testa, Joseph R.
Wei, Shuanzeng
author_facet Pei, Jianming
Zhao, Xiaofeng
Patchefsky, Arthur S.
Flieder, Douglas B.
Talarchek, Jacqueline N.
Testa, Joseph R.
Wei, Shuanzeng
author_sort Pei, Jianming
collection PubMed
description Accurate diagnoses of sarcoma are sometimes challenging on conventional histomorphology and immunophenotype. Many specific genetic aberrations including chromosomal translocations have been identified in various sarcomas, which can be detected by fluorescence in situ hybridization and polymerase chain reaction analysis. Next-generation sequencing-based RNA sequencing can screen multiple sarcoma-specific chromosome translocations/fusion genes in 1 test, which is especially useful for sarcoma without obvious differentiation. In this report, we utilized RNA sequencing on formalin-fixed paraffin-embedded (FFPE) specimens to investigate the possibility of diagnosing sarcomas by identifying disease-specific fusion genes. Targeted RNA sequencing was performed on 6 sarcoma cases. The expected genetic alterations (clear cell sarcoma/EWSR1-ATF1, Ewing sarcoma/EWSR1-FLI1, myxoid liposarcoma/DDIT3-FUS) in four cases were detected and confirmed by secondary tests. Interestingly, three SS18 fusion genes (SS18-SSX2B, SS18-SSX2, and SS18-SSX4) were identified in a synovial sarcoma case. A rare fusion gene (EWSR1-PATZ1) was identified in a morphologically challenging case; which enabled us to establish the diagnosis of low grade glioneural tumor. In conclusion, RNA sequencing on FFPE specimen is a reliable method in establishing the diagnosis of sarcoma in daily practice.
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spelling pubmed-66369672019-08-01 Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience Pei, Jianming Zhao, Xiaofeng Patchefsky, Arthur S. Flieder, Douglas B. Talarchek, Jacqueline N. Testa, Joseph R. Wei, Shuanzeng Medicine (Baltimore) Research Article Accurate diagnoses of sarcoma are sometimes challenging on conventional histomorphology and immunophenotype. Many specific genetic aberrations including chromosomal translocations have been identified in various sarcomas, which can be detected by fluorescence in situ hybridization and polymerase chain reaction analysis. Next-generation sequencing-based RNA sequencing can screen multiple sarcoma-specific chromosome translocations/fusion genes in 1 test, which is especially useful for sarcoma without obvious differentiation. In this report, we utilized RNA sequencing on formalin-fixed paraffin-embedded (FFPE) specimens to investigate the possibility of diagnosing sarcomas by identifying disease-specific fusion genes. Targeted RNA sequencing was performed on 6 sarcoma cases. The expected genetic alterations (clear cell sarcoma/EWSR1-ATF1, Ewing sarcoma/EWSR1-FLI1, myxoid liposarcoma/DDIT3-FUS) in four cases were detected and confirmed by secondary tests. Interestingly, three SS18 fusion genes (SS18-SSX2B, SS18-SSX2, and SS18-SSX4) were identified in a synovial sarcoma case. A rare fusion gene (EWSR1-PATZ1) was identified in a morphologically challenging case; which enabled us to establish the diagnosis of low grade glioneural tumor. In conclusion, RNA sequencing on FFPE specimen is a reliable method in establishing the diagnosis of sarcoma in daily practice. Wolters Kluwer Health 2019-06-21 /pmc/articles/PMC6636967/ /pubmed/31232935 http://dx.doi.org/10.1097/MD.0000000000016031 Text en Copyright © 2019 the Author(s). Published by Wolters Kluwer Health, Inc. http://creativecommons.org/licenses/by-nc/4.0 This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial License 4.0 (CCBY-NC), where it is permissible to download, share, remix, transform, and buildup the work provided it is properly cited. The work cannot be used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc/4.0
spellingShingle Research Article
Pei, Jianming
Zhao, Xiaofeng
Patchefsky, Arthur S.
Flieder, Douglas B.
Talarchek, Jacqueline N.
Testa, Joseph R.
Wei, Shuanzeng
Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience
title Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience
title_full Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience
title_fullStr Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience
title_full_unstemmed Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience
title_short Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience
title_sort clinical application of rna sequencing in sarcoma diagnosis: an institutional experience
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636967/
https://www.ncbi.nlm.nih.gov/pubmed/31232935
http://dx.doi.org/10.1097/MD.0000000000016031
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