Fast implementation of a scan statistic for identifying chromosomal patterns of genome wide association studies

Yan V. Sun, Douglas M. Jacobsen, Stephen T. Turner, Eric Boerwinkle and Sharon L.R. Kardia

Computational Statistics & Data Analysis, 2009, vol. 53, issue 5, 1794-1801

Abstract: In order to take into account the complex genomic distribution of SNP variations when identifying chromosomal regions with significant SNP effects, a single nucleotide polymorphism (SNP) association scan statistic was developed. To address the computational needs of genome wide association (GWA) studies, a fast Java application, which combines single-locus SNP tests and a scan statistic for identifying chromosomal regions with significant clusters of significant SNP effects, was developed and implemented. To illustrate this application, SNP associations were analyzed in a pharmacogenomic study of the blood pressure lowering effect of thiazide-diuretics (N=195) using the Affymetrix Human Mapping 100 K Set. 55,335 tagSNPs (pair-wise linkage disequilibrium R2

Date: 2009
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