The present disclosure provides a genome-wide association study method for imbalanced samples, including: randomly selecting L subsets from the healthy samples; pairing each of the L subsets with the diseased samples to obtain L sample combinations, and determining key genetic loci corresponding to each sample combination; evaluating a score of an importance degree of each sample combination according to times that each key genetic locus is determined in the L sample combinations; for each healthy sample, determining a mean value of scores of an importance degree of sample combinations that the healthy sample is assigned to, and determining the mean value as a confidence score of the healthy sample; and normalizing the confidence score of each healthy sample to obtain a weight of each healthy sample, and performing weighted logistic regression according to the weight of each healthy sample.
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