A fast and powerful aggregated Cauchy association test for joint analysis of multiple phenotypes

Pleiotropy is a widespread phenomenon in complex human diseases. Jointly analyzing multiple phenotypes can improve power performance of detecting genetic variants and uncover the underlying genetic mechanism.

This study aims to detect the association between genetic variants in a genomic region and multiple phenotypes.

We develop the aggregated Cauchy association test to detect the association between rare variants in a genomic region and multiple phenotypes (abbreviated as "Multi-ACAT"). Multi-ACAT first detects the association between each rare variant and multiple phenotypes based on reverse regression and obtains variant-level p-values, then takes linear combination of transformed p-values as the test statistic which approximately follows Cauchy distribution under the null hypothesis.

Extensive simulation studies show that when the proportion of causal variants in a genomic region is extremely small, Multi-ACAT is more powerful than the other several methods and is robust to bi-directional effects of causal variants. Finally, we illustrate our proposed method by analyzing two phenotypes [systolic blood pressure (SBP) and diastolic blood pressure (DBP)] from Genetic Analysis Workshop 19 (GAW19).

The Multi-ACAT computes extremely fast, does not consider complex distributions of multiple correlated phenotypes, and can be applied to the case with noise phenotypes.