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

Abstract

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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  • Authors+Show Affiliations

    ,

    Genomics Facility, Fox Chase Cancer Center.

    ,

    Department of Pathology and Laboratory Medicine, Temple University Hospital.

    ,

    Department of Pathology.

    ,

    Department of Pathology.

    ,

    Genomics Facility, Fox Chase Cancer Center.

    ,

    Genomics Facility, Fox Chase Cancer Center. Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA.

    Department of Pathology.

    Source

    Medicine 98:25 2019 Jun pg e16031

    MeSH

    Adult
    Biomarkers, Tumor
    Female
    Humans
    Male
    Middle Aged
    Paraffin Embedding
    Polymerase Chain Reaction
    Proto-Oncogene Proteins
    RNA-Binding Protein EWS
    Sarcoma
    Sequence Analysis, RNA
    Soft Tissue Neoplasms

    Pub Type(s)

    Case Reports
    Journal Article
    Observational Study

    Language

    eng

    PubMed ID

    31232935

    Citation

    Pei, Jianming, et al. "Clinical Application of RNA Sequencing in Sarcoma Diagnosis: an Institutional Experience." Medicine, vol. 98, no. 25, 2019, pp. e16031.
    Pei J, Zhao X, Patchefsky AS, et al. Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience. Medicine (Baltimore). 2019;98(25):e16031.
    Pei, J., Zhao, X., Patchefsky, A. S., Flieder, D. B., Talarchek, J. N., Testa, J. R., & Wei, S. (2019). Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience. Medicine, 98(25), pp. e16031. doi:10.1097/MD.0000000000016031.
    Pei J, et al. Clinical Application of RNA Sequencing in Sarcoma Diagnosis: an Institutional Experience. Medicine (Baltimore). 2019;98(25):e16031. PubMed PMID: 31232935.
    * Article titles in AMA citation format should be in sentence-case
    TY - JOUR T1 - Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience. AU - Pei,Jianming, AU - Zhao,Xiaofeng, AU - Patchefsky,Arthur S, AU - Flieder,Douglas B, AU - Talarchek,Jacqueline N, AU - Testa,Joseph R, AU - Wei,Shuanzeng, PY - 2019/6/25/entrez PY - 2019/6/25/pubmed PY - 2019/7/4/medline SP - e16031 EP - e16031 JF - Medicine JO - Medicine (Baltimore) VL - 98 IS - 25 N2 - 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. SN - 1536-5964 UR - https://www.unboundmedicine.com/medline/citation/31232935/Clinical_application_of_RNA_sequencing_in_sarcoma_diagnosis:_An_institutional_experience L2 - http://Insights.ovid.com/pubmed?pmid=31232935 DB - PRIME DP - Unbound Medicine ER -