Are rare variants really independent?

In this report, we show that two commonly used LD measures are not capable of detecting LD when rare variants are involved. We present this argument from two perspectives, both the LD measures themselves and the computational issues associated with them. To address these issues, we propose an alternative LD measure, the polychoric correlation, that was originally designed for detecting associations among categorical variables. Using simulated as well as the 1000 Genomes data, we explore the performances of LD measures in detail and discuss their implications in association studies.

Source: Genetic Epidemiology - March 16, 2017 Category: Epidemiology Authors: Asuman Turkmen, Shili Lin Tags: Brief Report Source Type: research