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Quick-multiplex-consensus (QMC)-PCR followed by high-resolution melting: a simple and robust method for mutation detection in formalin-fixed paraffin-embedded tissue
  1. Wakkas Fadhil1,
  2. Salih Ibrahem1,
  3. Rashmi Seth2,
  4. Mohammad Ilyas1,3
  1. 1Division of Pathology, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
  2. 2Department of Histopathology, Nottingham University Hospital NHS trust, Queen's Medical Centre, Nottingham, UK
  3. 3Nottingham Digestive Diseases Centre, NIHR Biomedical Research Unit, Queen's Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
  1. Correspondence to Professor Mohammad Ilyas, Division of Pathology, School of Molecular Medical Sciences, Queen's Medical Centre, Nottingham University, Nottingham NG7 2UH, UK; mohammad.ilyas{at}nottingham.ac.uk

Abstract

Background Mutation detection in tumours will become increasingly important in pathological diagnosis as ‘predictive’ mutations are identified. A cheap and reliable test that works on formalin-fixed paraffin-embedded (FFPE) tissue is required.

Methods The quick-multiplex-consensus (QMC)-PCR protocol was developed to be used with high-resolution melting (HRM) analysis. The assay was compared with Sanger sequencing. Robustness of the assay was tested in DNA from FFPE tissue.

Results QMC-PCR with HRM could detect a minimum of 2.5% of mutant alleles (compared with 20% detectable for Sanger sequencing). Ten mutation hotspots in KRAS, BRAF, PIK3CA and CDC4 were screened in 29 cell lines with 100% sensitivity and specificity. Forty-three FFPE colorectal tumours were sequenced for hotspots in KRAS and PIK3CA and then screened by QMC-PCR. There was 100% sensitivity, although, of 21 mutations detected by QMC-PCR, 16 were confirmed by sequencing (71% specificity, positive predictive value 76%). All 43 samples were then screened for mutations in all 10 hotspots. Of 430 tests, 43 (10%) showed aberrant melting and 36 were confirmed mutant (positive predictive value 84%). As our technique is more sensitive than direct sequencing, the remaining seven tests are probably sequencing false-negatives. Precision tests showed that there was little intra-assay and interassay variation.

Conclusions QMC-PCR with HRM is a simple, robust and inexpensive technique which had greater sensitivity than Sanger sequencing. It allows multiple mutation hotspots to be rapidly screened and is thus highly suited to mutation detection in DNA derived from FFPE tissues.

  • PCR
  • HRM
  • mutation detection
  • formalin-fixed paraffin-embedded
  • cancer genetics
  • DNA
  • molecular pathology

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Footnotes

  • Additional table and data are published online only at http://jcp.bmj.com/content/vol63/issue2

  • Funding University of Nottingham, Nottingham University Hospitals Charitable Trusts.

  • Competing interests None.

  • Ethics approval This study was conducted with the approval of the Oxfordshire REC B 05/Q1605/66.

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

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