Paper Info
Title
Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network.
Abstract
The future of medicine is moving towards the phase of precision medicine, with the goal to prevent and treat diseases by taking inter-individual variability into account. A large part of the variability lies in our genetic makeup. With the fast paced improvement of high-throughput methods for genome sequencing, a tremendous amount of genetics data have already been generated. The next hurdle for precision medicine is to have sufficient computational tools for analyzing large sets of data. Genome-Wide Association Studies (GWAS) have been the primary method to assess the relationship between single nucleotide polymorphisms (SNPs) and disease traits. While GWAS is sufficient in finding individual SNPs with strong main effects, it does not capture potential interactions among multiple SNPs. In many traits, a large proportion of variation remain unexplained by using main effects alone, leaving the door open for exploring the role of genetic interactions. However, identifying genetic interactions in large-scale genomics data poses a challenge even for modern computing.For this study, we present a new algorithm, Grammatical Evolution Bayesian Network (GEBN) that utilizes Bayesian Networks to identify interactions in the data, and at the same time, uses an evolutionary algorithm to reduce the computational cost associated with network optimization. GEBN excelled in simulation studies where the data contained main effects and interaction effects. We also applied GEBN to a Type 2 diabetes (T2D) dataset obtained from the Marshfield Personalized Medicine Research Project (PMRP). We were able to identify genetic interactions for T2D cases and controls and use information from those interactions to classify T2D samples. We obtained an average testing area under the curve (AUC) of 86.8 %. We also identified several interacting genes such as INADL and LPP that are known to be associated with T2D.Developing the computational tools to explore genetic associations beyond main effects remains a critically important challenge in human genetics. Methods, such as GEBN, demonstrate the utility of considering genetic interactions, as they likely explain some of the missing heritability.
Year
DOI
Venue
2016
10.1186/s13040-016-0094-4
BioData Mining
Keywords
Field
DocType
Bayesian Network,Discriminant analysis,Evolution algorithm,Genetic interactions,Type 2 diabetes
Data mining,Precision medicine,Evolutionary algorithm,Computer science,Genome-wide association study,Genomics,Genetic association,Bayesian network,Single-nucleotide polymorphism,DNA sequencing,Bioinformatics
Journal
Volume
Issue
ISSN
9
1
1756-0381
Citations 
PageRank 
References 
2
0.37
10
Authors
11
Name
Order
Citations
PageRank
Ruowang Li1184.15
Scott M. Dudek220626.27
Dokyoon Kim3706.32
Molly A Hall431.75
Yukiko Bradford521.39
Peggy Peissig618923.83
Murray Brilliant721.05
James G. Linneman8262.27
Catherine McCarty9416.13
Le Bao10122.35
Marylyn D. Ritchie1169286.79