Article Text

Download PDFPDF
The UK NEQAS for Molecular Genetics scheme for gastrointestinal stromal tumour: findings and recommendations following four rounds of circulation
  1. Newton A C S Wong1,
  2. Zandra C Deans2,
  3. Simon C Ramsden3
  1. 1Department of Histopathology, Bristol Royal Infirmary, Bristol, UK
  2. 2Department of Laboratory Medicine, UK NEQAS for Molecular Genetics, Royal Infirmary, Edinburgh, UK
  3. 3Department of Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester Foundation Trust, St. Mary's Hospital, Manchester, UK
  1. Correspondence to Dr Newton A C S Wong, Department of Histopathology, Bristol Royal Infirmary, Marlborough Street, Bristol BS2 8HW, UK; nacs.wong{at}


Aims To describe the UK NEQAS for Molecular Genetics scheme for gastrointestinal stromal tumour (GIST) and to report and interpret the findings of four rounds of circulation of this quality assurance programme for KIT/PDGFRA mutation analyses.

Methods Samples of GISTs from formalin-fixed paraffin-embedded tissue blocks were circulated to registered participants of the UK NEQAS for Molecular Genetics scheme for GIST. Three samples were provided per annual circulation from 2008 to 2011 inclusive. The participants were required to analyse the samples for KIT and/or PDGFRA mutations using their routine protocols, and the anonymised participants' reports were assessed and an annual scheme report issued.

Results The genotyping error rates for the 2008, 2009, 2010 and 2011 circulations were 13%, 33%, 19% and 4%, respectively. These errors were either missed or incorrectly described mutations. There was an overall false negative rate of 2% and false positive rate of 0%. The main recommendations that arose from these circulations were: (1) inclusion of reference accession numbers in reports; (2) avoidance of the term ‘heterozygous’ when analysing DNA from tumour tissue unless there was certainty that only neoplastic DNA was studied; and (3) the need to screen KIT exons 9, 11, 13 and 17 and PDGFRA exons 12, 14 and 18 before classifying a GIST as ‘wild type’.

Conclusions The UK NEQAS for Molecular Genetics scheme emphasises the potential complexities of KIT/PDGFRA mutation analyses for GISTs and provides recommendations to help optimise such genotyping and reporting. The scheme has also demonstrated its educational value among participating laboratories.

  • Gastrointestinal stromal tumours
  • kit proto-oncogene protein
  • PDGF-R-alpha
  • genotyping techniques
  • quality assurance
  • histopathology
  • molecular pathology
  • gastrointestinal disease

Statistics from

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.


  • Competing interests ZD has received educational grants from Astra Zeneca and Roche. NACSW has received educational grants from Novartis and has received lecturing honoraria from Novartis and Pfizer.

  • Ethics approval The paper reports how well participant laboratories analysed circulated tumour tissue samples for specific mutations. The tumours were derived from human patients but were anonymised at source. The genotyping was performed as part of a quality assurance program and not as a scientific study.

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