An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

ABSTRACT:

Background

Possible single nucleotide polymorphism (SNP) interactions in breast cancer are usually not investigated in genome-wide association studies. Previously, we proposed a particle swarm optimization (PSO) method to compute these kinds of SNP interactions. However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions.

Methodology/principal findings

In this study, we propose IPSO algorithm to improve the reliability of PSO for the identification of the best protective SNP barcodes (SNP combinations and genotypes with maximum difference between cases and controls) associated with breast cancer. SNP barcodes containing different numbers of SNPs were computed. The top five SNP

SUBMITTER: Chuang LY 

PROVIDER: S-EPMC3356401 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature