title: The application of next-generation sequencing-based molecular diagnostics in endometrial stromal sarcoma.
abstract: OBJECTIVE
  Endometrial stromal sarcomas (ESSs) are divided into low-grade and high-grade subtypes, with the latter showing more aggressive clinical behaviour. Although histology and immunophenotype can aid in the diagnosis of these tumours, genetic studies can provide additional diagnostic insights, as low-grade ESSs frequently harbour fusions involving JAZF1/SUZ12 and/or JAZF1/PHF1, whereas high-grade ESSs are defined by YWHAE-NUTM2A/B fusions. The aim of this study was to evaluate the utility of a next-generation sequencing (NGS)-based assay in identifying ESS fusions in archival formalin-fixed paraffin-embedded tumour samples.
  
  
  RESULTS
  We applied an NGS-based fusion transcript detection assay (Archer FusionPlex Sarcoma Panel) that targets YWHAE and JAZF1 fusions in a series of low-grade ESSs (n = 11) and high-grade ESSs (n = 5) that were previously confirmed to harbour genetic rearrangements by fluorescence in-situ hybridization (FISH) and/or reverse transcription polymerase chain reaction (RT-PCR) analyses. The fusion assay identified junctional fusion transcript sequences that corresponded to the known FISH/RT-PCR results in all cases. Four low-grade ESSs harboured JAZF1-PHF1 fusions with different junctional sequences, and all were correctly identified because of the open-ended nature of the assay design, using anchored multiplex polymerase chain reaction. Seven non-ESS sarcomas were also included as negative controls, and no strong ESS fusion candidates were identified in these cases.
  
  
  CONCLUSIONS
  Our findings demonstrate good sensitivity and specificity of an NGS-based gene fusion assay in the detection of ESS fusion transcripts.
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
authors.forename: Mona
authors.initials: M
authors.lastname: Anand
authors.affiliation: ArcherDX, Inc., Boulder, CO, USA.
authors.forename: Josh D
authors.initials: JD
authors.lastname: Haimes
authors.affiliation: ArcherDX, Inc., Boulder, CO, USA.
authors.forename: Namitha
authors.initials: N
authors.lastname: Manoj
authors.affiliation: ArcherDX, Inc., Boulder, CO, USA.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Berlin
authors.affiliation: ArcherDX, Inc., Boulder, CO, USA.
authors.forename: Brian A
authors.initials: BA
authors.lastname: Kudlow
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
authors.forename: Marisa R
authors.initials: MR
authors.lastname: Nucci
authors.affiliation: Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada.
authors.forename: Tony L
authors.initials: TL
authors.lastname: Ng
authors.affiliation: Department of Histopathology, King Edward Memorial Hospital and School for Women's and Infants' Health, University of Western Australia, Perth, WA, Australia.
authors.forename: Colin J R
authors.initials: CJ
authors.lastname: Stewart
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada. chlee2@ualberta.ca.|Department of Laboratory Medicine and Pathology, Royal Alexandra Hospital, Edmonton, AB, Canada. chlee2@ualberta.ca.
authors.forename: Cheng-Han
authors.initials: CH
authors.lastname: Lee
mesh_terms: D000328:Adult; D000368:Aged; D016889:Endometrial Neoplasms / Q000175:diagnosis* / Q000235:genetics; D036821:Endometrial Stromal Tumors / Q000175:diagnosis* / Q000235:genetics; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008875:Middle Aged; D015514:Oncogene Proteins, Fusion / Q000032:analysis*; D057089:Pathology, Molecular; D018203:Sarcoma, Endometrial Stromal / Q000175:diagnosis* / Q000235:genetics; D012680:Sensitivity and Specificity; D055815:Young Adult
chemical_list: D015514:Oncogene Proteins, Fusion
keywords: FAM22A; FAM22B; JAZF1; NUTM2A; NUTM2B; PHF1; SUZ12; YWHAE; endometrial stromal sarcoma; genetic fusion