A method for detecting the presence or absence of a nucleic acid sequence to be detected at a predetermined locus on a chromosome, the method comprising:
- (2) a step of detecting, via a digital PCR method, the presence or absence of hybridization, to a genomic DNA fragment derived from the chromosome, of
- a first probe nucleic acid that hybridizes to all or part of the nucleic acid sequence to be detected, and
- a second probe nucleic acid that hybridizes to a nucleic acid sequence other than the nucleic acid sequence to be detected in the predetermined locus;
- and
- (3) a step of detecting the presence of the nucleic acid sequence to be detected at the predetermined locus when the first probe nucleic acid and the second probe nucleic acid are hybridized to the genomic DNA fragment and double-positive is detected, and
- of detecting the absence of the nucleic acid sequence to be detected at the predetermined locus when double-positive is not detected.