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Motivated by genetic association studies of SNPs with genotype uncertainty,we propose a generalization of the Kruskal-Wallis test that incorporates groupuncertainty when comparing k samples. The extended test statistic is based onprobability-weighted rank-sums and follows an asymptotic chi-squaredistribution with k-1 degrees of freedom under the null hypothesis. Simulationstudies confirm the validity and robustness of the proposed test in finitesamples. Application to a genome-wide association study of type 1 diabeticcomplications further demonstrates the utilities of this generalizedKruskal-Wallis test for studies with group uncertainty.

A Generalized Kruskal-Wallis Test Incorporating Group Uncertainty with Application to Genetic Association Studies