Gene | N | SNPs | Single SNP p-value | Linear p-value | IBS p-value | Quadratic p-value |
---|
IL6 block 1 | 219 | 3 | 0.018 | 0.021 | 0.057 | 0.0038 |
IL10 block 2 | 219 | 7 | 0.10 | 0.181 | 0.083 | 0.021 |
IRAK3 block 1 | 216 | 15 | 0.0048 | 0.070 | 0.044 | 0.16 |
VEGFA block 1 | 218 | 6 | 0.0035 | 0.77 | 0.032 | 0.056 |
ANGPT2 block 2â€
|
207
|
12
|
2.54E-05
|
4.5E-05
|
3.4E-05
|
1.0E-06
|
- In subjects of African ancestry, kernel machine regression detected significant ALI association for 4 ALI candidate genes: IL6, IL10, IRAK3, and VEGFA. The results of each of 3 kernel functions – linear, identity by state (IBS), and quadratic – are listed, and are contrasted with the most extreme individual SNP result for the block in question. Individual SNP results for the genes IRAK3 and VEGFA demonstrated a more extreme association with ALI than the haplotype block as tested by kernel function. However, the individual SNPs detected were not the same SNPs as have been previously associated with ALI [14, 41]. In addition, results of kernel regression are reported for ANGPT2(†); single SNP and haplotype association of ANGPT2 with ALI has previously been reported for this population [13]. We include these results to demonstrate that the kernel method remains effective in the presence of strong individual SNP results. N: number of subjects with complete data; SNPs: number of SNPs per ALI-associated block.