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Background  Approximately 10–15 % of gastrointestinal stromal tumors (GISTs) lack gain of function mutations in the  KIT  and  platelet-derived growth factor receptor alpha  ( PDGFRA ) genes. An alternate mechanism of oncogenesis through loss of function of the succinate-dehydrogenase (SDH) enzyme complex has been identified for a subset of these “wild type” GISTs.    Methods  Paired tumor and normal DNA from an SDH-intact wild-type GIST case was subjected to whole exome sequencing to identify the pathogenic mechanism(s) in this tumor. Selected findings were further investigated in panels of GIST tumors through Sanger DNA sequencing, quantitative real-time PCR, and immunohistochemical approaches.    Results  A hemizygous frameshift mutation (p.His2261Leufs*4), in the  neurofibromin 1  ( NF1)  gene was identified in the patient’s GIST; however, no germline  NF1  mutation was found. A somatic frameshift mutation (p.Lys54Argfs*31) in the  MYC associated factor X  ( MAX ) gene was also identified. Immunohistochemical analysis for MAX on a large panel of GISTs identified loss of MAX expression in the  MAX -mutated GIST and in a subset of mainly  KIT -mutated tumors.    Conclusion  This study suggests that inactivating  NF1  mutations outside the context of neurofibromatosis may be the oncogenic mechanism for a subset of sporadic GIST. In addition, loss of function mutation of the  MAX  gene was identified for the first time in GIST, and a broader role for MAX in GIST progression was suggested.    Electronic supplementary material  The online version of this article (doi:10.1186/s12885-015-1872-y) contains supplementary material, which is available to authorized users.

Somatic loss of function mutations in neurofibromin 1 and MYC associated factor X genes identified by exome-wide sequencing in a wild-type GIST case