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Utility of sarcoma-specific fusion gene analysis in paraffin-embedded material for routine diagnosis at a specialist centre
  1. Khin Thway1,
  2. Sasha Rockcliffe1,
  3. David Gonzalez2,
  4. John Swansbury2,
  5. Toon Min2,
  6. Lisa Thompson2,
  7. Cyril Fisher1
  1. 1Department of Histopathology, Royal Marsden Hospital, London, UK
  2. 2Department of Haemato-Oncology, Royal Marsden Hospital, Sutton, Surrey, UK
  1. Correspondence to Dr Khin Thway, Department of Histopathology, Royal Marsden NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; khin.thway{at}


Aims Diagnosis of soft tissue sarcomas can be difficult. It can be aided by detection of specific genetic aberrations in many cases. This study assessed the utility of a molecular genetics/cytogenetics service as part of the routine diagnostic service at the Royal Marsden Hospital.

Methods A retrospective audit was performed over a 15-month period to evaluate the diagnostic usefulness for soft tissue sarcomas with translocations of fluorescence in situ hybridisation (FISH) and reverse-transcriptase PCR (RT-PCR) in paraffin-embedded (PE) material. Results were compared with histology, and evaluated.

Results Molecular investigations were performed on PE material in 158 samples (total 194 RT-PCR and 174 FISH tests), of which 85 were referral cases. Synovial sarcoma, Ewing sarcoma and low-grade fibromyxoid sarcoma were the most commonly tested tumours. Myxoid liposarcoma showed the best histological and molecular concordance, and alveolar rhabdomyosarcoma showed the best agreement between methods. FISH had a higher sensitivity for detecting tumours (73%, compared with 59% for RT-PCR) with a better success rate than RT-PCR, although the latter was specific in identifying the partner gene for each fusion. In particular, referral blocks in which methods of tissue fixation and processing were not certain resulted in higher RT-PCR failure rates.

Conclusions FISH and RT-PCR on PE tissue are practical and effective ancillary tools in the diagnosis of soft tissue sarcomas. They are useful in confirming doubtful histological diagnoses and excluding malignant diagnoses. PCR is less sensitive than FISH, and the use of both techniques is optimal for maximising the detection rate of translocation-positive sarcomas.

  • Audit
  • FISH
  • molecular genetics
  • sarcoma
  • soft tissue tumours

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  • Funding We acknowledge NHS funding to the NIHR Biomedical Research Centre.

  • Competing interests None.

  • Provenance and peer review Not commissioned; externally peer reviewed.