›› See also Haplotype Trend Regression
›› See also Haplotype Frequency Estimation

Haplotype association analysis is particularly useful in scanning across a large SNP map to locate markers that correlate with a response. Figures 1 and 2 show -log(p) plots of the significance of genetic markers in predicting the response. Figure 1 shows the significance of relating individual genetic markers to a response. Because there is little information in a given SNP, the signal in the first 50 markers stands out poorly. Figure 2 is a haplotype test with haplotypes composed of a moving window of five genetic markers. Note how the signal stands out clearly in the neighborhood of markers 12-40 in Figure 2, but is barely visible in Figure 1. Each p-value in Figure 2 is the significance of performing a regression estimate of the response, based on haplotype frequencies. The haplotypes can be constructed over a range of one or more genetic markers. One can include or exclude markers based on deactivating columns in the spreadsheet view.

 

Figure 1. Genotype analysis p-value plot

Figure 2. Haplotype analysis p-value plot