The phenomenon whereby genetic factors at a particular locus are shared between two or more traits (not to be confused with declaring the exact causal variant). Tests for genetic colocalization try to separate between two scenarios: (i) there is a causal variant for trait A that is distinct from the causal variant for trait B, whilst being at the same locus, and (ii) the causal variant for trait A and trait B are shared. A variety of algorithms exist for distinguishing between these scenarios, typically by looking for concordance of effects across all SNPs at the locus at both traits.
Genetic colocalization of a locus between two traits is necessary but not sufficient for a causal relationship, and it can be thought of an MR analysis performed with a SNP but with an added sensitivity analysis in which we are trying to rule out the possibility that there are two distinct causal variants in the same region. The approach is regularly used to infer putative causal relationships between ‘omic variables and complex traits. Often an assumption of these algorithms is that there is only one causal variant in the region, which may not be appropriate.
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