Figure 1.
Diagram Illustrating How Statistical Significance for a Set of SNPs Is Calculated in HYST
Vertical bars denote SNPs. When two blocks are on different chromosomes or far away on the same chromosome, the blocks can be assumed to be independent, that is, LD r2 between the two key SNPs of the two blocks equals zero. Step 1: define n blocks of SNPs according to LD and/or gene information; step 2: compute a block-based p value in each block by GATES and mark the SNPs from which the block-based p value is derived (the broad-brush in the plot); step 3: combine the n block-based p values by using scaled chi-square test, correcting for LD among the n key SNPs.