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  • Comparison between two different next generation sequencing platforms for clinical relevant gene mutation test in solid tumours

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Comparison between two different next generation sequencing platforms for clinical relevant gene mutation test in solid tumours
  1. Silvia Bessi1,
  2. Francesco Pepe2,
  3. Marco Ottaviantonio1,
  4. Pasquale Pisapia2,
  5. Umberto Malapelle2,
  6. Giancarlo Troncone2,
  7. Mauro Biancalani1
  1. 1 Azienda USL Toscana Centro, Complex Unit of Pathological Anatomy Empoli-Prato, S. Stefano Hospital, Prato, Italy
  2. 2 Department of Public Health, University of Naples Federico II, Naples, Italy
  1. Correspondence to Dr Silvia Bessi, Azienda USL Toscana Centro, Complex Unit of Pathological Anatomy Empoli-Prato, Prato 59100, Italy; silvia2.bessi{at}uslcentro.toscana.it

Abstract

In the present study, we analysed 44 formalin fixed paraffin embedded (FFPE) from different solid tumours by adopting two different next generation sequencing platforms: GeneReader (QIAGEN, Hilden, Germany) and Ion Torrent (Thermo Fisher Scientific, Waltham, Massachusetts, USA). We highlighted a 100% concordance between the platforms. In addition, focusing on variant detection, we evaluated a very good agreement between the two tests (Cohen’s kappa=0.84) and, when taking into account variant allele fraction value for each variant, a very high concordance was obtained (Pearson’s r=0.94). Our results underlined the high performance rate of GeneReader on FFPE samples and its suitability in routine molecular predictive practice.

  • tumour markers
  • oncology
  • molecular biology

https://doi.org/10.1136/jclinpath-2019-206422

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    Footnotes

    • Handling editor Runjan Chetty.

    • Twitter @PasqualePisapia

    • Contributors SB, UM, GT and MB conceived the study; SB and FP performed the experimental part; all authors contributed as molecular pathologists; all authors wrote, reviewed and 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 for publication Written informed consent was obtained from all patients and documented in accordance with the general authorisation to process personal data for scientific research purposes from ‘The Italian Data Protection Authority’ (http://www.garanteprivacy.it/web/guest/home/docweb/-/docwebdisplay/export/2485392).

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