All three FGFR1 alterations identified in WT GIST are known to be deleterious (K656E, FGFR1-HOOK3 and FGFR1-TACC1 fusions) in contrast to 1/5 FGFR1 alterations in the non WT GIST (amplification—Additional file 1: Table S8), thus suggesting that the FGFR1 alterations are more likely drivers in the WT GIST. This evidence concerns the gene HOOK3 and gastrointestinal stromal tumor.