Background::
Genome-Wide Association Study (GWAS) plays a very important role in
identifying the causes of a disease. Because most of the existing methods for genetic-interaction
detection in GWAS are designed for a single-correlation model, their performances vary
considerably for different disease models. These methods usually have high computation cost and
low accuracy.
Method::
We present a new multi-objective heuristic optimization methodology named HSMMGKG
for detecting genetic interactions. In HS-MMGKG, we use harmony search with five
objective functions to improve the efficiency and accuracy. A new strategy based on p-value and
MDR is adopted to generate more reasonable results. The Boolean representation in BOOST is
modified to calculate the five functions rapidly. These strategies take less time complexity and
have higher accuracy while detecting the potential models.
Results::
We compared HS-MMGKG with CSE, MACOED and FHSA-SED using 26 simulated
datasets. The experimental results demonstrate that our method outperforms others in accuracy and
computation time. Our method has identified many two-locus SNP combinations that are
associated with seven diseases in WTCCC dataset. Some of the SNPs have direct evidence in CTD
database. The results may be helpful to further explain the pathogenesis.
Conclusion::
It is anticipated that our proposed algorithm could be used in GWAS which is helpful
in understanding disease mechanism, diagnosis and prognosis.