KATE is a program that employs hierarchical clustering and kernel based association testing to analyse the effects of low frequency and rare variants on quantitative traits within a chromosomal region.
Single-point analysis of low-frequency and rare variants is under-powered, as not enough copies of the minor allele are observed. An alternative approach is to use methods that combine information across multiple low frequency or rare variant sites within a region. Focusing on the analysis of quantitative traits, we developed KATE (Kernel Association Test Extended) that uses the Allele Match kernel to cluster individuals into disjoint clusters and tests the cluster-specific effects via ANOVA.
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Rare variant association testing for next-generation sequencing data via hierarchical clustering.
Human heredity 2012;74;3-4;165-71