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Potential pitfalls in multiplex PCR-based next-generation sequencing: a case-based report
  1. Jack K Tung1,
  2. Kelly A Devereaux2,
  3. Archana Lal Erdmann3,
  4. Iris Schrijver1,
  5. James Zehnder1,
  6. Carlos J Suarez1
  1. 1Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
  2. 2Department of Pathology, NYU Grossman School of Medicine, New York City, New York, USA
  3. 3GeneCode, Mountain View, California, USA
  1. Correspondence to Carlos J Suarez, Department of Pathology, Stanford University School of Medicine, Stanford, USA; cjsuarez{at}


Amplicon-based next-generation sequencing (NGS) assays employ highly sensitive, rapid, and cost-effective methods to detect clinically actionable mutations for the diagnosis, prognosis, and treatment of patients with cancer. However, recognition of certain limitations inherent to amplicon-based NGS assays is crucial for the correct interpretation and reporting of variants in the clinical setting. In this report, we illustrate three different potential pitfalls related to amplicon-based NGS assays based on our institutional experience and highlight how the risk of such events can be minimised.

  • pathology
  • molecular
  • medical oncology
  • genes
  • neoplasm
  • genetics

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  • Handling editor Runjan Chetty.

  • JKT and KAD contributed equally.

  • Contributors JKT, KAD and CJS participated in the design and analysis of data for this manuscript. All authors participated in the writing of this manuscript.

  • Funding This study was funded by: NCI 2PO 1CA49605 (JZ) and the Stanford University School of Medicine, department of Pathology.

  • Competing interests None declared.

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