Fig. 1: Illustration of the joint tagging effect as an artefact generator for statistical epistasis. | Nature Communications

Fig. 1: Illustration of the joint tagging effect as an artefact generator for statistical epistasis.

From: Performance of deep-learning-based approaches to improve polygenic scores

Fig. 1

Here, SNP1 and SNP2 imperfectly tag (r2 > 0) the untyped SNP3, which is the causal variant affecting the phenotype Y. This pattern can arise even if the r2 between SNP1 and SNP2 is zero. Statistical epistasis may only be generated by this pattern if the SNP1–SNP2 haplotype is a better tag for SNP3 than either SNP individually.

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