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Molecular profiling of gene fusions in soft tissue sarcomas by Ion AmpliSeq(TM): a study of 35 cases

BACKGROUND: The accurate diagnosis of sarcoma can be difficult as there are over 70 different subtypes. While molecular profiling in soft tissue sarcoma (STS) has gradually been incorporated into routine diagnostics, conventional methods such as fluorescence in situ hybridization (FISH), reverse tra...

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Autores principales: Wei, Rong, Gao, Feng, Zeng, Zixin, Gui, Ziwei, Shang, Yangwei, Shen, Ningning, Wang, Ziyue, Han, Weixia, Shen, Honghong, Li, Xin, E, Li, Ma, Wenxia, Wang, Chen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: AME Publishing Company 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8990829/
https://www.ncbi.nlm.nih.gov/pubmed/35402176
http://dx.doi.org/10.21037/tcr-22-70
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author Wei, Rong
Gao, Feng
Zeng, Zixin
Gui, Ziwei
Shang, Yangwei
Shen, Ningning
Wang, Ziyue
Han, Weixia
Shen, Honghong
Li, Xin
E, Li
Ma, Wenxia
Wang, Chen
author_facet Wei, Rong
Gao, Feng
Zeng, Zixin
Gui, Ziwei
Shang, Yangwei
Shen, Ningning
Wang, Ziyue
Han, Weixia
Shen, Honghong
Li, Xin
E, Li
Ma, Wenxia
Wang, Chen
author_sort Wei, Rong
collection PubMed
description BACKGROUND: The accurate diagnosis of sarcoma can be difficult as there are over 70 different subtypes. While molecular profiling in soft tissue sarcoma (STS) has gradually been incorporated into routine diagnostics, conventional methods such as fluorescence in situ hybridization (FISH), reverse transcriptase-PCR (RT-PCR), and Sanger sequencing have several drawbacks. By allowing simultaneous analysis of multiple targets and increasing sequencing depth to achieve ultra-sensitivity, next-generation sequencing (NGS) can not only detect common genetic abnormalities without prior assumptions but also identify uncommon or even new variants. METHODS: In this study, the applicability of NGS in assessing STS using the Ion Torrent Proton was evaluated and compared with other methods. A cohort of 35 tissue specimens from STS patients, including alveolar soft-part sarcoma (ASPS), Ewing’s sarcoma (ES), synovial sarcoma (SS), dermatofibrosarcoma protuberans (DFSP), and myxoid liposarcoma (MLPS) patients, were subjected to NGS by an Ion AmpliSeqTM Custom panel. RESULTS: A proportion of 97.14% (34/35) were successfully conducted to detect gene fusion positive events and met all criteria for good quality. The concordance between NGS and conventional techniques was 94.12% (32/34). NGS also showed superior results, as Sanger sequencing and FISH in two cases were false negatives, demonstrating the excellent diagnostic utility of NGS for translocation detection in STS. CONCLUSIONS: The results in this study show the potential for NGS to aid in diagnosis and clinical monitoring of STS and warrant additional studies in larger cohorts.
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spelling pubmed-89908292022-04-09 Molecular profiling of gene fusions in soft tissue sarcomas by Ion AmpliSeq(TM): a study of 35 cases Wei, Rong Gao, Feng Zeng, Zixin Gui, Ziwei Shang, Yangwei Shen, Ningning Wang, Ziyue Han, Weixia Shen, Honghong Li, Xin E, Li Ma, Wenxia Wang, Chen Transl Cancer Res Original Article BACKGROUND: The accurate diagnosis of sarcoma can be difficult as there are over 70 different subtypes. While molecular profiling in soft tissue sarcoma (STS) has gradually been incorporated into routine diagnostics, conventional methods such as fluorescence in situ hybridization (FISH), reverse transcriptase-PCR (RT-PCR), and Sanger sequencing have several drawbacks. By allowing simultaneous analysis of multiple targets and increasing sequencing depth to achieve ultra-sensitivity, next-generation sequencing (NGS) can not only detect common genetic abnormalities without prior assumptions but also identify uncommon or even new variants. METHODS: In this study, the applicability of NGS in assessing STS using the Ion Torrent Proton was evaluated and compared with other methods. A cohort of 35 tissue specimens from STS patients, including alveolar soft-part sarcoma (ASPS), Ewing’s sarcoma (ES), synovial sarcoma (SS), dermatofibrosarcoma protuberans (DFSP), and myxoid liposarcoma (MLPS) patients, were subjected to NGS by an Ion AmpliSeqTM Custom panel. RESULTS: A proportion of 97.14% (34/35) were successfully conducted to detect gene fusion positive events and met all criteria for good quality. The concordance between NGS and conventional techniques was 94.12% (32/34). NGS also showed superior results, as Sanger sequencing and FISH in two cases were false negatives, demonstrating the excellent diagnostic utility of NGS for translocation detection in STS. CONCLUSIONS: The results in this study show the potential for NGS to aid in diagnosis and clinical monitoring of STS and warrant additional studies in larger cohorts. AME Publishing Company 2022-03 /pmc/articles/PMC8990829/ /pubmed/35402176 http://dx.doi.org/10.21037/tcr-22-70 Text en 2022 Translational Cancer Research. All rights reserved. https://creativecommons.org/licenses/by-nc-nd/4.0/Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.
spellingShingle Original Article
Wei, Rong
Gao, Feng
Zeng, Zixin
Gui, Ziwei
Shang, Yangwei
Shen, Ningning
Wang, Ziyue
Han, Weixia
Shen, Honghong
Li, Xin
E, Li
Ma, Wenxia
Wang, Chen
Molecular profiling of gene fusions in soft tissue sarcomas by Ion AmpliSeq(TM): a study of 35 cases
title Molecular profiling of gene fusions in soft tissue sarcomas by Ion AmpliSeq(TM): a study of 35 cases
title_full Molecular profiling of gene fusions in soft tissue sarcomas by Ion AmpliSeq(TM): a study of 35 cases
title_fullStr Molecular profiling of gene fusions in soft tissue sarcomas by Ion AmpliSeq(TM): a study of 35 cases
title_full_unstemmed Molecular profiling of gene fusions in soft tissue sarcomas by Ion AmpliSeq(TM): a study of 35 cases
title_short Molecular profiling of gene fusions in soft tissue sarcomas by Ion AmpliSeq(TM): a study of 35 cases
title_sort molecular profiling of gene fusions in soft tissue sarcomas by ion ampliseq(tm): a study of 35 cases
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8990829/
https://www.ncbi.nlm.nih.gov/pubmed/35402176
http://dx.doi.org/10.21037/tcr-22-70
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