title: Ancillary molecular analysis in the diagnosis of soft tissue tumours: reassessment of its utility at a specialist centre.
abstract: OBJECTIVE
  The histological diagnosis of soft tissue tumours (STTs) can be difficult, sometimes requiring a combination of morphology, immunophenotype and ancillary molecular tests. Many STTs are associated with characteristic genetic aberrations that can be assessed using fluorescence in situ hybridisation (FISH), reverse transcription-PCR (RT-PCR) or mutational analysis. We have previously assessed the practicality and sensitivity of using these modalities as part of the routine diagnosis of STT in paraffin-embedded material and now revisit the subject in light of further experience in this field.
  
  
  METHODS
  200 consecutive cases from 2013 that had undergone FISH, RT-PCR or mutational analysis were assessed to evaluate their diagnostic utility compared with preliminary histological assessment.
  
  
  RESULTS
  218 FISH, 91 RT-PCR and 43 mutational analysis tests were performed. Compared with the previous study, FISH for MDM2 amplification in possible well-differentiated/dedifferentiated liposarcomas, and mutational analysis for assessing KIT, PDGFR and BRAF mutations made up a large proportion of the workload (107 and 43 tests, respectively). As in the previous study, alveolar rhabdomyosarcoma showed the best FISH:RT-PCR concordance. Unlike previously, RT-PCR showed marginally higher sensitivity than FISH (78.9% and 76.9%), while continuing to demonstrate higher specificity (90.9% and 84.3%). RT-PCR again showed an increased failure rate (5.5%; 1% for FISH).
  
  
  CONCLUSIONS
  We demonstrate the continuing utility of RT-PCR and FISH for STT diagnosis, and that each has advantages in specific contexts. These ancillary molecular tests are important tools in both defining and excluding diagnoses of STT, which is crucial in determining prognosis and guiding appropriate management.
authors.affiliation: Sarcoma Unit, Royal Marsden Hospital, London, UK.
authors.forename: Katherine
authors.initials: K
authors.lastname: Vroobel
authors.affiliation: Department of Molecular Diagnostics, Royal Marsden Hospital, Sutton, Surrey, UK.
authors.forename: David
authors.initials: D
authors.lastname: Gonzalez
authors.affiliation: Department of Molecular Diagnostics, Royal Marsden Hospital, Sutton, Surrey, UK.
authors.forename: Dorte
authors.initials: D
authors.lastname: Wren
authors.affiliation: Department of Molecular Diagnostics, Royal Marsden Hospital, Sutton, Surrey, UK.
authors.forename: Lisa
authors.initials: L
authors.lastname: Thompson
authors.affiliation: Department of Clinical Cytogenetics, Royal Marsden Hospital, Sutton, Surrey, UK.
authors.forename: John
authors.initials: J
authors.lastname: Swansbury
authors.affiliation: Sarcoma Unit, Royal Marsden Hospital, London, UK.
authors.forename: Cyril
authors.initials: C
authors.lastname: Fisher
authors.affiliation: Sarcoma Unit, Royal Marsden Hospital, London, UK.
authors.forename: Khin
authors.initials: K
authors.lastname: Thway
mesh_terms: D000720:Ancillary Services, Hospital; D004252:DNA Mutational Analysis; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008080:Liposarcoma / Q000175:diagnosis* / Q000378:metabolism; D016612:Paraffin Embedding; D051736:Proto-Oncogene Proteins c-mdm2 / Q000235:genetics / Q000378:metabolism*; D012189:Retrospective Studies; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012983:Soft Tissue Neoplasms / Q000175:diagnosis* / Q000378:metabolism
chemical_list: C497206:MDM2 protein, human; D051736:Proto-Oncogene Proteins c-mdm2
keywords: FISH; MOLECULAR PATHOLOGY; SOFT TISSUE; SOFT TISSUE TUMOURS