Building Bayesian networks from GWAS statistics based on Independence of Causal Influence

Genome-wide association studies (GWASs) have received an increasing attention to understand genotype-phenotype relationships. In this paper, we study how to build Bayesian networks from publicly released GWAS statistics to explicitly reveal the conditional dependency between single-nucleotide polymorphisms (SNPs) and traits. The key challenge in building a Bayesian network is the specification of the conditional probability table (CPT) of an variable with multiple parent variables. We employ the Independence of Causal Influences (ICI) which assumes that the causal mechanism of each parent variable is mutually independent. Specifically, we derive a formulation from the Noisy-or model, one of the ICI models, to specify the CPT using the released GWAS statistics. We prove that the specified CPT is accurate as long as the underlying individual-level genotype and phenotype profile data follows the Noisy-or model. We empirically evaluate the Noisy-or model and its derived formulation using data from openSNP. Experimental results demonstrate the effectiveness of our approach.