Bayesian Network Construction and Genotype-Phenotype Inference Using GWAS Statistics

Genome-wide association studies (GWASs) have received increasing attention to understand how genetic variation affects different human traits. In this paper, we study whether and to what extent exploiting the GWAS statistics can be used for inferring private information about a human individual. We first provide a method to construct a three-layered Bayesian network explicitly revealing the conditional dependency between single-nucleotide polymorphisms (SNPs) and traits from public GWAS catalog. The key challenge in building a Bayesian network from GWAS statistics is the specification of the conditional probability table of a variable with multiple parent variables. We employ the models of independence of causal influences which assume that the causal mechanism of each parent variable is mutually independent. We then formulate three inference problems based on the dependency relationship captured in the Bayesian network, namely trait inference given SNP genotype, genotype inference given trait, and trait inference given known traits, and develop efficient formulas and algorithms. Different from previous work, the possible target of these inference problems we study may be any individual, not limited to GWAS participants. Empirical evaluations show the effectiveness of our proposed methods. In summary, our work implies that meaningful information can be inferred from modeling GWAS statistics, and appropriate privacy protection mechanisms need to be developed to protect genetic privacy not only of GWAS participants but also regular individuals.