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Performance analysis of SiRe next-generation sequencing panel in diagnostic setting: focus on NSCLC routine samples
  1. Francesco Pepe1,
  2. Caterina De Luca1,
  3. Riccardo Smeraglio1,
  4. Pasquale Pisapia1,
  5. Roberta Sgariglia1,
  6. Mariantonia Nacchio1,
  7. Maria Russo1,
  8. Nicola Serra1,
  9. Danilo Rocco2,
  10. Ciro Battiloro2,
  11. Francesca Ambrosio3,
  12. Gianluca Gragnano1,
  13. Elena Vigliar1,
  14. Claudio Bellevicine1,
  15. Giancarlo Troncone1,
  16. Umberto Malapelle1
  1. 1 Department of Public Health, University of Naples Federico II, Naples, Italy
  2. 2 Oncology, A.O.R.N. Vincenzo Monaldi, Naples, Italy
  3. 3 Oncology, A.O.R.N. Antonio Cardarelli, Naples, Italy
  1. Correspondence to Professor Giancarlo Troncone, Department of Public Health, University of Naples Federico II, Naples 5 I-80131, Italy; giancarlo.troncone{at}unina.it

Abstract

Aims Following the development for liquid biopsies of the SiRe next-generation sequencing (NGS) panel that covers 568 clinical relevant mutations in EGFR, KRAS, NRAS, BRAF, cKIT and PDGFRa genes, in this current study, we apply this small NGS panel on tissue samples of lung cancer.

Methods A total of 322 specimens were prospectively tested. Technical parameters were analysed on both cytological and histological samples. In a subset of 75 samples, the EGFR SiRe results were compared with those generated by the European Community (CE)–IVD EGFR assay on Idylla platform. Clinical outcomes of 11 patients treated, on the basis of SiRe results, were also evaluated.

Results Only 28 (8.7%) specimens failed to produce a library; out of the 294 remaining samples, a total of 168 somatic mutations were found. In nearly all instances (74/75–99%), the EGFR SiRe results were confirmed by Idylla. In general, SiRe analytical parameters were excellent. However, histological and cytological specimens differed in relation to average reads for sample, mean number of mapped reads, median read length and average reads for amplicon. Treatment outcome evaluation in 11 patients showed a partial response in 82 % (9/11) patients with a median progression-free survival of 340 days.

Conclusions The small gene panel SiRe is a clinically relevant tool useful to widespread the adoption of NGS in predictive molecular pathology laboratories.

  • NSCLC
  • NGS
  • predictive molecular pathology

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Footnotes

  • FP and CDL contributed equally.

  • Handling editor Professor Runjan Chetty.

  • Contributors FP, CDL, GT and UM conceived the study and wrote the paper. RiS, RoS, MN, MR and GG performed the experimental part. PP, EV and ClB contributed as pathologists. DR, CiB and FA contributed as oncologists. NS performed the statistical analysis. All Authors approved the final version of the manuscript.

  • Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

  • Competing interests None declared.

  • Patient consent Obtained

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

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