Title :
Strategies for pathway-based analysis of genome-wide SNP data
Author :
Patumcharoenpol, P. ; Chan, Jeffrey ; Prom-On, S. ; Meechai, Asawin
Author_Institution :
Bioinf. & Syst. Biol. Program, King Mongkut´s Univ. of Technol. Thonburi, Bangkok, Thailand
Abstract :
Numerous genome-wide association studies (GWAS) have been performed in order to determine the susceptible loci of diseases. However, most diseases still cannot be explained by a single locus. Pathway-based methods address this problem by combining those small effects into groups of related genes or pathways. However, because pathway-based approaches consist of multiple steps, there is much room for improvement. This paper presents an improved method for translating list of SNPs from GWAS into list of genes. We incrementally adjusted and compared different modifications applied to Parkinson´s disease (PD) genome-wide SNP data and then used GSEA-P to analyze the resulting list of genes. After careful adjustments, we are able to identify more relevant pathways that were not found previously.
Keywords :
diseases; genomics; GSEA-P; Parkinson disease; genome wide SNP data; genome wide association studies; pathway based analysis; Bioinformatics; Cancer; Databases; Genomics; Parkinson´s disease; Parkinson´s disease; genome-wide association; linkage disequilibrium; pathway-based approach;
Conference_Titel :
Defense Science Research Conference and Expo (DSR), 2011
Conference_Location :
Singapore
Print_ISBN :
978-1-4244-9276-3
DOI :
10.1109/DSR.2011.6026801