Table 3.
Identification of haplotypes in localized haplotype clusters that are associated with high myopia
|
Markers & haplotypes* |
Haplotype counts |
Haplotype being considered |
All other haplotypes |
Fisher's exact test |
||||
|---|---|---|---|---|---|---|---|---|
| Total no.† | no. in cluster (%) | Controls† | Cases† | Controls | Cases | Pvalue‡ | OR (95% CI) § | |
|
Sample Set 1 for cases defined by SE ≤-12 diopters Marker = rs220168 (S47), Cluster = 0.G | ||||||||
| Markers: S47 |
|
|
|
|
|
|
|
|
| G (2) |
202 |
28 (13.9%) |
155 |
47 |
557 |
135 |
0.2744 |
1.25 (0.83 - 1.85) |
| Markers: S47-S48 | ||||||||
| GC (21) |
35 |
26 (74.3%) |
22 |
13 |
690 |
169 |
0.0176 |
2.41 (1.09 - 5.12) |
| GT (22) |
167 |
2 (1.2%) |
133 |
34 |
579 |
148 |
1.0000 |
1.00 (0.63 - 1.54) |
| Markers: S47-S48-S49 | ||||||||
| GCT (211) |
25 |
25 (100.0%) |
13 |
12 |
699 |
170 |
0.0015 |
3.78 (1.54 - 9.19) |
| GCC (212) |
10 |
1 (10.0%) |
9 |
1 |
703 |
181 |
0.6965 |
0.43 (0.01 - 3.15) |
| GTC (222) |
23 |
2 (8.7%) |
17 |
6 |
695 |
176 |
0.4411 |
0.39 (0.44 - 3.77) |
| Markers: S47-S48-S49-S50 |
|
|
|
|
|
|
|
|
| GCTC (2112) |
13 |
13 (100.0%) |
8 |
5 |
704 |
177 |
0.1546 |
2.48 (0.63 - 8.73) |
| GCTT (2111) |
12 |
12 (100.0%) |
5 |
7 |
707 |
175 |
0.0041 |
5.64 (1.52 - 22.82) |
| GCCC (2122) |
10 |
1 (10.0%) |
9 |
1 |
703 |
181 |
0.6965 |
0.43 (0.01 - 3.15) |
| GTCC (2222) |
3 |
2 (66.7%) |
1 |
2 |
711 |
180 |
0.1071 |
7.87 (0.41 – 465.3) |
|
Sample Set 2 for cases defined by SE ≤ -10 diopters Marker = rs3819142 (S54), Cluster = 0.C | ||||||||
| Markers: S54 |
|
|
|
|
|
|
|
|
| C (2) |
290 |
222 (76.6%) |
193 |
97 |
595 |
441 |
0.0055 |
0.68 (0.51 - 0.90) |
| Markers: S49-S54 | ||||||||
| TC (12) |
253 |
214 (84.6%) |
166 |
87 |
622 |
451 |
0.0274 |
0.72 (0.54 - 0.97) |
| CC (22) | 37 | 8 (21.6%) | 27 | 10 | 761 | 528 | 0.0926 | 0.43 (0.23 - 1.15) |
*Markers are rs220168 (S47), rs220170 (S48), rs11911271 (S49), rs220171 (S50) and rs3819142 (S54) along the 5’ end to the 3’ end direction of the sense strand of the UMODL1 gene. A localized haplotype cluster is indicated in the format of “(node number).(allele of the marker being considered)”. For example, “Marker = rs220168 (S47), Cluster = 0.G” refers to the G allele of the marker S47 at node “0” (zero). The allele of each marker is shown in both the ACGT and the 1–2 formats (1 being the major and 2 the minor allele). For each localized haplotype cluster found to be associated with high myopia by Beagle, the table here shows the haplotypes for an increasing number of markers until the haplotypes account for all or almost all of the association signals for the cluster and give the lowest P values (in boldface) for the Fisher’s exact test. Then, haplotypes are shown for one extra window with one additional marker just to show that one additional marker does not provide additional information and the P values for Fisher’s exact test become less impressive (i.e. larger).
†For a particular haplotype under consideration, the total count is the sum of the counts in both controls and cases.
‡Note that the P values for the Fisher’s exact test are not corrected for multiple testing because the cluster2haps program is only used to identify the haplotypes involved in the haplotype clusters that are already found positive by Beagle after adjustment by permutations for multiple comparisons.
§The odds ratio (OR) is calculated for the haplotype being considered with regard to all other haplotypes as the reference. The 95% confidence intervals (CI) are also shown.