A graphical assessment of p-values from sliding window haplotype tests of association to identify asthma susceptibility loci on chromosome 11q
1 Genometrics Section, Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Balitmore, USA
2 Johns Hopkins Asthma and Allergy Center, Johns Hopkins University School of Medicine, Baltimore, USA
3 Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, USA
4 Department of Microbiology, Howard University College of Medicine, Baltimore, USA
5 Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, USA
BMC Genetics 2006, 7:38 doi:10.1186/1471-2156-7-38Published: 14 June 2006
Past work on asthmatic African American families revealed a strong linkage peak with modest evidence of association on chromosome 11q. Here, we perform tests of association for asthma and a panel of 609 SNPs in African American subjects using a sliding window approach. While efficient in screening a region of dense genotyping, this approach does create some problems: high numbers of tests, assimilating thousands of results, and questions about setting priorities on regions with association signals.
We present a newly developed tool, Graphical Assessment of Sliding P-values or GrASP, which uses color display to indicate the width of the sliding windows, significance of individual tests, density of SNP coverage and location of known genes that simplifies some of these issues, and use it to identify regions of interest in these data.
We demonstrate that GrASP makes it easier to visualize, summarize and prioritize regions of interest from sliding window haplotype analysis, based jointly on the p-value from all the tests from these windows and the building of haplotypes of significance in the region. Using this approach, five regions yielded strong evidence for linkage and association with asthma, including the prior peak linkage region.