An Improved PSO Algorithm for Generating Protective SNP Barcodes in Breast Cancer

Li-Yeh Chuang, Yu-Da Lin, Hsueh-Wei Chang and Cheng-Hong Yang

PLOS ONE, 2012, vol. 7, issue 5, 1-9

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 barcode results are retained for computing the next SNP barcode with a one-SNP-increase for each processing step. Based on the simulated data for 23 SNPs of six steroid hormone metabolisms and signalling-related genes, the performance of our proposed IPSO algorithm is evaluated. Among 23 SNPs, 13 SNPs displayed significant odds ratio (OR) values (1.268 to 0.848; p

Date: 2012
References: View complete reference list from CitEc
Citations: View citations in EconPapers (4)

Downloads: (external link)
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0037018 (text/html)
https://journals.plos.org/plosone/article/file?id= ... 37018&type=printable (application/pdf)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0037018

DOI: 10.1371/journal.pone.0037018

Access Statistics for this article

More articles in PLOS ONE from Public Library of Science
Bibliographic data for series maintained by plosone ().