Detecting epistasis via Markov bases

Detecting high-order epistasis in nonlinear

7 High-order epistasis has been observed in many genotype-phenotype maps. These multi-way inter8 actions could have profound implications for evolution and may be useful for dissecting complex 9 traits. Previous analyses have assumed a linear genotype-phenotype map, and then applied a linear 10 high-order epistasis model to dissect epistasis. The assumption of linearity has not been tested 11 i...

Detecting Epistasis in Genome-wide Association Studies with the Marginal EPIstasis Test

Epistasis, commonly defined as the interaction between multiple genes, is an important genetic component underlying phenotypic variation. Many statistical methods have been developed to model and identify epistatic interactions between genetic variants. However, because of the large combinatorial search space of interactions, most epistasis mapping methods face enormous computational challenges...

Detecting epistasis with the marginal epistasis test in genetic mapping studies of quantitative traits

Epistasis, commonly defined as the interaction between multiple genes, is an important genetic component underlying phenotypic variation. Many statistical methods have been developed to model and identify epistatic interactions between genetic variants. However, because of the large combinatorial search space of interactions, most epistasis mapping methods face enormous computational challenges...

Computing Markov bases, Gröbner bases, and extreme rays

Hill-climbing through “random chemistry” for detecting epistasis

There are estimated to be on the order of 10 single nucleotide polymorphisms (SNPs) existing as standing variation in the human genome. Certain combinations of these SNPs can interact in complex ways to predispose individuals for a variety of common diseases, even though individual SNPs may have no ill effects. Detecting these epistatic combinations is a computationally daunting task. Trying to...