Discovering SNP Interactions Associated with Breast Cancer Using Evolutionary Algorithms

Genetic association is a challenging task for the identification and characterization of genes that increase the susceptibility to common complex multifactorial diseases. To fully execute genetic studies of complex diseases, modern geneticists face the challenge of detecting interactions between loci. In this paper, two evolutionary methods were compared to detect associations of single nucleotide polymorphisms (SNPs): a genetic algorithm and Gauss particle swarm optimization. Genetic algorithm was developed with partial matched crossover operator and two different strategies for initialization: regular initialization and top-5 strategy initialization. In both methods for different SNP barcodes (SNP combinations with their corresponding genotypes) the difference between case and control data is computed systematically. The algorithms look for the best combination which is the barcode with maximum difference between the two groups. Analysis results support that the genetic algorithm with top-5 strategy for initialization provides higher frequency difference values than the Gauss particle swarm optimization. It is also proved that a genetic algorithm reduces a computational cost for obtaining higher frequency difference between the case and control group.