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Poster Display session 1

3914 - Clinical validation of a novel assay for the detection of diagnostic alterations in sarcomas


28 Sep 2019


Poster Display session 1


Tumour Site



Lauren Mc Connell


Annals of Oncology (2019) 30 (suppl_5): v683-v709. 10.1093/annonc/mdz283


L. Mc Connell1, O. Houghton2, M. Catherwood3, J. Gazdova4, P. Stewart5, A. Oniscu6, P. Groenen7, L. Kroeze7, P. Taniere8, A. Flanagan9, A. Stobl9, M. Salto-Tellez4, D. Gonzalez De Castro4

Author affiliations

  • 1 Genomic Medicine, Centre for Cancer Research and Cell Biology - Queen's University Belfast, BT71AE - Belfast/GB
  • 2 Pathology, Belfast Health and Social Care Trust, Belfast/GB
  • 3 Haematology, Belfast Health and Social Care Trust, Belfast/GB
  • 4 Precision Medicine Centre, Centre for Cancer Research and Cell Biology - Queen's University Belfast, BT9 7AB - Belfast/GB
  • 5 Genomic Medicine, Centre for Cancer Research and Cell Biology - Queen's University Belfast, Belfast/GB
  • 6 Pathology, Royal Infirmary of Edinburgh, Edinburgh/GB
  • 7 Pathology, Radboud University Medical Center, Nijmegen/NL
  • 8 Pathology, Queen Elizabeth-University Hospital Birmingham NHS Foundation Trust, B15 2TH - Birmingham/GB
  • 9 Pathology, Royal National Orthopaedic Hospital, London/GB


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Abstract 3914


Sarcoma is a rare disease affecting both bone and connective tissue and with over 100 pathologic entities, diagnosis can be difficult. Approximately one third of sarcoma patients however are characterised by recurrent genetic alterations mainly chromosomal translocations, which result in fusion genes, and gene amplifications. Fusion genes are highly useful diagnostic markers and are currently identified in the clinical setting using FISH/RT-PCR. Conversely, conclusive results cannot be achieved in up to 25% of fusion positive patients using these methods. Next generation sequencing (NGS) is a promising tool that can improve soft-tissue sarcoma diagnosis.


A novel sarcoma-specific NGS gene capture panel containing probes for 90 fusion genes and 7 genes with frequent copy number changes was designed, optimised and validated in order to improve fusion-positive sarcoma diagnosis. Genomic DNA was extracted from 92 well-characterised FFPE samples and libraries prepared using the KAPA Hyperplus kit (Roche) and hybridised using the SeqCap Hybridisation kit (Roche) and sequenced on a NextSeq platform (Illumina).


Sarcoma specific translocations or gene amplifications were identified in 92 out of 94 cases giving the targeted gene panel a sensitivity of approximately 98% and specificity of 100% (Table).Table:

1717P Sarcoma tumour types and number of cases with structural variants or copy number variations detected

Soft Tissue Tumour TypeNo. of casesSV/CNV detected
Synovial Sarcoma2525
Alveolar Rhabdomyosarcoma66
Well/Dedifferentiated Liposarcoma98
Intimal Sarcoma11
Desmoplastic Small Round Cell Tumour (DSRCT)22
Ewing’s Sarcoma1111
Inflammatory Myofibroblastic Tumour22
Myxoid Liposarcoma 1010
Chondroid Lipoma11
Clear Cell Sarcoma44
Epithelioid Haemangioendothelioma21
Low-grade Fibromyxoid Sarcoma33
Nodular Fasciitis11
Alveolar Soft Part Cell Sarcoma 11
Congenital Fibrosarcoma 22
Solitary Fibrous Tumour22
Aneurysmal Bone Cyst11
BCOR-CCNB3 Sarcoma11
Extraskeletal Myxoid Chondrosarcoma55
Mesenchymal Chondrosarcoma22
Dermatofibrosarcoma Protuberans (DFSP)33


To the best of our knowledge this is the first sarcoma-specific NGS panel validated in FFPE-derived genomic DNA. It is at least as sensitive and specific as the combination of FISH and RT-PCR and can be implemented in routine clinical diagnostic workflows. We are currently investigating whether fusion genes can be detected in plasma using ctDNA from 14 patients and results will be reported at the conference.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

David Gonzalez de Castro.


Sarcoma UK.


All authors have declared no conflicts of interest.

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