Table 2. .
Age and Sex Adjusted Haplotype Association Analysis in AMD Patients and Controls
|
Haplotype* |
% Frequencies (95% CI)† |
OR (95% CI)‡ |
P |
| Block 1 (1q32), CFH: rs800292-rs1410996 | |||
| A–C | 37.71 (34.1, 41.32) | Ref | |
| G–C | 3.63 (2.53, 4.73) | 4.45 (2.32, 8.55) | 0.0000§ |
| A–T | 4.69 (3.49, 5.89) | 4.18 (1.99, 8.75) | 0.0002§ |
| G–T | 53.97 (50.21, 57.74) | 1.70 (1.20, 2.41) | 0.0029§ |
| Block 2 (6p21.3), C2/CFB: rs9332739-rs4151667 | |||
| G–T | 97.32 (96.13, 98.51) | Ref | |
| G–A | 0.41 (0.19, 0.63) | 8.86 (1.88, 41.69) | 0.0058§ |
| C–T | 0.50 (0.15, 0.84) | 3.84 (0.74, 20.02) | 0.1102 |
| C–A | 1.78 (0.67, 2.89) | 0.37 (0.07, 2.05) | 0.2546 |
| Block 3 (19p13.2), C3: rs2241394-rs2230199 | |||
| G–C | 91.1 (88.95, 93.26) | Ref | |
| G–G | 8.07 (6.05, 10.09) | 0.87 (0.49, 1.55) | 0.6445 |
| C–G | 0.60 (0.01, 1.19) | 0.95 (0.16, 5.50)¶ | 0.9514 |
| C–C | 0.23 (0.00, 0.62) | ||
*
The risk haplotypes are noted in roman font, and the protective haplotypes are noted in italic font.
†
The frequencies of haplotypes, from subsequent iterations of the EM algorithm in hapassoc (an open sources R package), were estimated based on the genotype data from all subjects combined.
‡
The ORs, listed in descending order, were age- and sex-adjusted in generalized linear models (GLM) by using the hapassoc package.
§
ORs with P < 0.05.
¶
Two rare haplotypes of block 3 (rs2241394–rs2230199), C–G and C–C, were pooled together to prevent estimation algorithm failed to converge due to very low frequency of rare alleles.