A polynucleotide, which is a novel causative gene for cancer, is elucidated, and, based on this finding, provided are a method for detecting the polynucleotide, or a polypeptide encoded by the polynucleotide; a kit and a primer set for the detection; a method for screening an inhibitor of the polypeptide; and a pharmaceutical composition for treating a cancer containing the inhibitor. In the detection method of the present invention, an NTRK3 fusion protein, or a fusion gene encoding the fusion protein, or an ETV6 fusion protein, or a fusion gene encoding the fusion protein, in a sample derived from the digestive system obtained from a subject, is detected.