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Genotype Correlation Analysis Reveals Pathway-Based Functional Disequilibrium and Potential Epistasis in the Human
William S Bush1, Jonathan L Haines2
1Center for Human Genetics Research, Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.
Applications of Evolutionary Computation : 17Th European Conference, Evoapplications 2014, Granada, Spain, April 23-25, 2014 : Revised Selected Papers. Evoapplications (Conference) (17Th : 2014 : Granada, Spain)
|April 11, 2017
Summary
Epistasis, or gene interaction, is key to complex traits. This study identified 453 gene pairs with strong evidence of epistasis within biological pathways, offering insights into complex disease origins.
Area of Science:
- Genetics and Systems Biology
- Investigating gene-gene interactions within biological networks.
Background:
- Epistasis (gene interaction) is crucial for understanding complex phenotypes and diseases.
- Biological pathways integrate gene functions, making them key areas to study epistasis.
Purpose of the Study:
- To characterize functional dependencies between alleles in the human interactome using KEGG pathways.
- To identify gene pairs exhibiting epistasis within the context of biological functions.
Main Methods:
- Utilized genotype data from the International HapMap Project.
- Performed chi-square tests to detect non-independence between single nucleotide polymorphism (SNP) pairs.
- Employed haplotype-based Transmission Disequilibrium Test (TDT) to assess skewed pseudo-haplotype transmission.
Main Results:
- Identified biological pathways enriched for functional disequilibrium.
- Discovered 863 SNP pairs (453 gene pairs) showing consistent non-independence and transmission distortion.
- These findings provide strong evidence for epistasis in functionally related gene pairs.
Conclusions:
- Epistasis plays a significant role in complex phenotypes.
- Identifying epistatic gene pairs within pathways can illuminate the etiology of complex diseases.
- This study provides a valuable resource of gene pairs with strong evidence of functional epistasis.