You are here

Article Text

Article menu
Short report
Use of the GeneReader NGS System in a clinical pathology laboratory: a comparative study
  1. Ulrike Koitzsch1,
  2. Carina Heydt1,
  3. Hans Attig2,
  4. Isabelle Immerschitt1,
  5. Sabine Merkelbach-Bruse1,
  6. Alessandro Fammartino2,
  7. Reinhard H Büttner1,3,
  8. Yi Kong1,
  9. Margarete Odenthal1,3
  1. 1Institute of Pathology, University Hospital of Cologne, Cologne, Germany
  2. 2QIAGEN GmbH, Hilden, Germany
  3. 3Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
  1. Correspondence to Dr Margarete Odenthal, Institute of Pathology, University Hospital of Cologne, Kerpener Str. 62, Koeln 50924, Germany; m.odenthal{at}uni-koeln.de

Abstract

Despite its successful use in academic research, next-generation sequencing (NGS) still represents many challenges for routine clinical adoption due to its inherent complexity and specialised expertise typically required to set-up, test and operate a complete workflow.This study aims to evaluate QIAGEN's newly launched GeneReader NGS System solution in a pathology laboratory setting by assessing the system's ease of use, sequencing accuracy and data reproducibility. Our laboratory was able to implement the system and validate its performance using clinical samples in direct comparison to an approved Sanger sequencing platform and to an alternative in-house NGS technology. The QIAGEN workflow focuses on clinically actionable hotspots maximising testing efficiency. Combined with automated upstream sample processing and integrated downstream bioinformatics, it offers a realistic solution for pathology laboratories with limited prior experience in NGS technology.

  • TUMOUR MARKERS
  • MOLECULAR ONCOLOGY
  • MOLECULAR PATHOLOGY
  • LABORATORY MANAGEMENT
  • METHODOLOGY

This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/

https://doi.org/10.1136/jclinpath-2017-204342

Statistics from Altmetric.com

    Request Permissions

    If you wish to reuse any or all of this article please use the link below which will take you to the Copyright Clearance Center’s RightsLink service. You will be able to get a quick price and instant permission to reuse the content in many different ways.

    View Full Text

    Supplementary materials

    • Abstract in German

      This web only file has been produced by the BMJ Publishing Group from an electronic file supplied by the author(s) and has not been edited for content.

    Footnotes

    • UK and CH contributed equally.

    • Handling editor Runjan Chetty

    • Contributors UK and HA performed the GeneReader workflow, whereas CH, SM-B performed NGS by the conventional in-house workflow. CH, II and UK validated data by Sanger sequencing, and AF, RB and MO performed data interpretation and illustration. RHB, AF, YK, CH and MO wrote the manuscript, which was then reviewed by all authors.

    • Competing interests The University Hospital of Cologne, Institute of Pathology is in a collaboration agreement with Qiagen (Hilden, Germany). Reinhard H Büttner is on the Advisory Board of Qiagen The authors declare no other conflict of interest. As of December 2016, the sequencing chemistry used in this study is not available in the USA.

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