Identification of fusion transcripts in sarcoma from archival formalin‐fixed paraffin‐embedded tissues: A next‐generation sequencing approach

Most sarcomas are highly aggressive, and cause necrosis and hemorrhage. The diagnosis of sarcoma is challenging because of the lack of specificity of immunohistochemical staining; however, molecular biological approaches, such as genetic mutation, chromosomal translocation, and gene amplification, a...

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Published inPathology international Vol. 72; no. 9; pp. 444 - 456
Main Authors Fujii, Tomomi, Takeda, Maiko, Uchiyama, Tomoko, Nitta, Yuji, Maebou, Katsuya, Terada, Chiyoko, Okada, Fumi, Matsuoka, Minami, Sugimoto, Sumire, Sasaki, Shoh, Morita, Kohei, Itami, Hiroe, Miyake, Makito, Takeda, Masayuki, Sawabata, Noriyoshi, Fujimoto, Kiyohide, Ohbayashi, Chiho
Format Journal Article
LanguageEnglish
Published Tokyo Wiley Subscription Services, Inc 01.09.2022
Subjects
Chromosome translocations
Complementary DNA
DNA
Fluorescence
Fluorescence in situ hybridization
Formaldehyde
Fusion protein
Gene amplification
Genes
Hemorrhage
Mutation
Necrosis
NGS
Paraffin
Paraffins
PCR
Polymerase chain reaction
Reverse transcription
Ribonucleic acid
RNA
Sarcoma
stored FFPE tissue
Tissues
Translocation
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Summary:Most sarcomas are highly aggressive, and cause necrosis and hemorrhage. The diagnosis of sarcoma is challenging because of the lack of specificity of immunohistochemical staining; however, molecular biological approaches, such as genetic mutation, chromosomal translocation, and gene amplification, are promising. In this study, we extracted RNA from formalin‐fixed paraffin‐embedded (FFPE) tissue derived from surgically resected specimens of sarcoma stored for various periods and performed next‐generation sequencing (NGS) analysis by MiniSeq using the Archer Fusion‐Plex Sarcoma Panel. RNA was extracted from 63 FFPE tissue samples, and the degree of RNA degradation was assessed. The number of reads and fragment lengths were evaluated by NGS analysis. RNA extraction and cDNA synthesis were successful in 56 cases and library preparation was possible. Fusion genes were detected in 16 of 63 archived FFPE tissue samples in this study. However, in 18 cases, fragmentation was strong, and high‐quality libraries could not be obtained. Nevertheless, comprehensive analysis of fusion genes with high sequence specificity by NGS can be a powerful alternative to reverse transcription‐polymerase chain reaction and fluorescence in situ hybridization methods.
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ISSN:1320-5463
1440-1827
DOI:10.1111/pin.13265