Genomics Inform.  2018 Dec;16(4):e38. 10.5808/GI.2018.16.4.e38.

HisCoM-GGI: Software for Hierarchical Structural Component Analysis of Gene-Gene Interactions

• Choi S
• Lee S
• Park T

• KMID: 2439228
• DOI: http://doi.org/10.5808/GI.2018.16.4.e38

Abstract

Gene-gene interaction (GGI) analysis is known to play an important role in explaining missing heritability. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in a case-control design. In this study, we developed "Hierarchical structural CoMponent analysis of Gene-Gene Interactions" (HisCoM-GGI) software for GGI analysis with a continuous phenotype. The HisCoM-GGI method considers hierarchical structural relationships between genes and single nucleotide polymorphisms (SNPs), enabling both gene-level and SNP-level interaction analysis in a single model. Furthermore, this software accepts various types of genomic data and supports data management and multithreading to improve the efficiency of genome-wide association study data analysis. We expect that HisCoM-GGI software will provide advanced accessibility to researchers in genetic interaction studies and a more effective way to understand biological mechanisms of complex diseases.

Keyword

gene-gene interactions; generalized structured component analysis; genome-wide association study; ridge regression

MeSH Terms

Case-Control Studies
Genome-Wide Association Study
Methods
Phenotype
Polymorphism, Single Nucleotide
Statistics as Topic