ORIGINAL ARTICLE—ALIMENTARY TRACT A quality control program for mutation detection in KIT and PDGFRA in gastrointestinal stromal tumours Isabelle Hostein • Maria Debiec-Rychter • Sylvianne Olschwang • Pierre-Paul Bringuier • Louisa Toffolati • David Gonzalez • Se ´bastien Forget • Fabienne Escande • Lucyna Morzuch • Elena Tamborini • Nicolas Faur • Silvana Pilotti • Paolo Dei Tos • Jean-Franc ¸ois Emile • Jean-Michel Coindre Received: 13 August 2010 / Accepted: 27 December 2010 / Published online: 1 February 2011 Ó Springer 2011 Abstract Background Although most gastrointestinal stromal tumours (GIST) carry oncogenic mutations in KIT exons 9, 11, 13 and 17, or in platelet-derived growth factor receptor alpha (PDGFRA) exons 12, 14 and 18, around 10% of GIST are free of these mutations. Genotyping and accurate detection of KIT/PDGFRA mutations in GIST are becom- ing increasingly useful for clinicians in the management of the disease. Method To evaluate and improve laboratory practice in GIST mutation detection, we developed a mutational screening quality control program. Eleven laboratories were enrolled in this program and 50 DNA samples were analysed, each of them by four different laboratories, giving 200 mutational reports. Results In total, eight mutations were not detected by at least one laboratory. One false positive result was reported in one sample. Thus, the mean global rate of error with clinical implication based on 200 reports was 4.5%. Con- cerning specific polymorphisms detection, the rate varied from 0 to 100%, depending on the laboratory. The way mutations were reported was very heterogeneous, and some errors were detected. Conclusion This study demonstrated that such a program was necessary for laboratories to improve the quality of the analysis, because an error rate of 4.5% may have clinical consequences for the patient. Electronic supplementary material The online version of this article (doi:10.1007/s00535-011-0375-0) contains supplementary material, which is available to authorized users. I. Hostein (&) Á N. Faur Á J.-M. Coindre Department of Pathology, Institut Bergonie ´, 229 cours de l’Argonne, 33076 Bordeaux cedex, France e-mail: hostein@bergonie.org M. Debiec-Rychter Department of Human Genetics, University of Leuven, Leuven, Belgium S. Olschwang Centre de Recherche en Cance ´rologie de Marseille INSERM U891, Institut Paoli-Calmettes, Marseille, France P.-P. Bringuier Laboratory of Pathology, Edouard Herriot Hospital, Lyon, France L. Toffolati Á P. Dei Tos Department of Pathology, CA Foncello Hospital, Treviso, Italy D. Gonzalez Department of Hemato-Oncology, The Institute of Cancer Research, Sutton, UK S. Forget Department of Biology and Pathology, Institute of Cancerology Gustave Roussy, Paris, France F. Escande Biology and Pathological Laboratory, Lille Hospital, Lille, France L. Morzuch Department of Biology and Genetics, Medical University of Gdansk, Gdan ´sk, Poland E. Tamborini Á S. Pilotti Laboratory of Experimental Pathology, Foundation IRCCS Tumor Institute, Milan, Italy J.-F. Emile Department of Pathology, Ambroise Pare Hospital, Boulogne, France 123 J Gastroenterol (2011) 46:586–594 DOI 10.1007/s00535-011-0375-0