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Clinical application of RNA sequencing in sarcoma diagnosis: An institutional experience.
Medicine (Baltimore) 2019; 98(25):e16031M

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.

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.

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://dx.doi.org/10.1097/MD.0000000000016031 DB - PRIME DP - Unbound Medicine ER -