Table 5. Replication and pooled analysis: SNP association with ALS outcome, including and excluding WTCCC2 controls.
| Discovery analysis | Replication analysis | Pooled analysis | |||||||
| Chr | SNP | pos (build 36) | Closest gene (distance) | OR (95% CI) | P | OR (95% CI) | p | OR (95% CI) | p |
| Without WTCCC2 controls | |||||||||
| 4 | rs4833346 | 127584779 | FAT4 (951 kb) | 1.5 (1.2, 1.9) | 1.2E-04 | 1.1 (0.8, 1.5) | 0.43 | 1.4 (1.2, 1.6) | 2.1E-05 |
| 20 | rs6075164 | 16985876 | PCSK2 (169 kb) | 0.7 (0.5, 0.8) | 1.8E-04 | 0.8 (0.7, 0.9) | 0.0016 | 0.7 (0.6, 0.8) | 3.7E-05 |
| 20 | rs6080539 | 16977494 | PCSK2 (177 kb) | 0.6 (0.5, 0.8) | 1.1E-04 | 0.7 (0.6, 0.8) | 5.0E-05* | 0.7 (0.6, 0.8) | 5.1E-05 |
| 8 | rs7000234 | 81699669 | ZNF704 (4 kb) | 2.0 (1.3, 3.1) | 8.6E-04 | 1.8 (1.4, 2.4) | 6.1E-05* | 1.7 (1.3, 2.3) | 1.5E-04 |
| 20 | rs6080544 | 16987959 | PCSK2 (167 kb) | 0.7 (0.5, 0.8) | 2.0E-04 | 1.0 (0.8, 1.4) | 0.78 | 0.7 (0.6, 0.9) | 1.9E-04 |
| 4 | rs3113494 | 88051625 | LOC100506746 (13 kb) | 0.7 (0.6, 0.8) | 1.9E-04 | 0.7 (0.6, 0.9) | 9.6E-05* | 0.8 (0.6, 0.9) | 2.0E-04 |
| 11 | rs2278170 | 4453422 | OR52K1 (13 kb) | 0.7 (0.5, 0.8) | 5.5E-04 | 0.7 (0.6, 0.9) | 8.0E-04 | 0.7 (0.6, 0.9) | 2.4E-04 |
| 6 | rs1190270 | 105731108 | POPDC3 | 0.5 (0.3, 0.7) | 1.8E-04 | 0.6 (0.4, 0.8) | 4.0E-04 | 0.6 (0.4, 0.8) | 2.7E-04 |
| 8 | rs6985069 | 28142007 | ELP3 (37 kb) | 0.7 (0.6, 0.9) | 6.0E-03 | 0.7 (0.6, 0.9) | 3.3E-04 | 0.7 (0.6, 0.9) | 2.7E-04 |
| 11 | rs9633905 | 4453189 | OR52K1 (13 kb) | 0.7 (0.5, 0.8) | 5.9E-04 | 0.8 (0.6, 0.9) | 8.9E-04 | 0.7 (0.6, 0.9) | 4.3E-04 |
| With WTCCC2 controls | |||||||||
| 4 | rs3113494 | 88051625 | LOC100506746 (13 kb) | 0.7 (0.6, 0.9) | 2.8E-04 | 0.7 (0.6, 0.9) | 9.6E-05* | 0.7 (0.6, 0.8) | 9.0E-07 |
| 11 | rs2278170 | 4453422 | OR52K1 (13 kb) | 0.8 (0.6, 0.9) | 0.0020 | 0.7 (0.6, 0.9) | 8.0E-04 | 0.7 (0.6, 0.8) | 6.7E-06 |
| 3 | rs17253119 | 54905813 | CACNA2D3 | 0.6 (0.5, 0.9) | 0.0028 | 0.7 (0.5, 0.9) | 0.011 | 0.6 (0.5, 0.8) | 1.8E-05 |
| 6 | rs1190270 | 105731108 | POPDC3 | 0.5 (0.3, 0.7) | 1.3E-04 | 0.6 (0.4, 0.8) | 4.0E-04 | 0.6 (0.4, 0.7) | 3.6E-05 |
| 18 | rs7242525 | 34364676 | LOC647946 (676 kb) | 0.6 (0.5, 0.7) | 6.0E-06 | 0.7 (0.6, 0.9) | 0.0043 | 0.7 (0.5, 0.8) | 1.1E-04 |
| 4 | rs4833346 | 127584779 | FAT4 (951 kb) | 1.4 (1.2, 1.6) | 9.8E-05 | 1.1 (0.8, 1.5) | 0.43 | 1.3 (1.1, 1.5) | 1.7E-04 |
| 20 | rs6080539 | 16977494 | PCSK2 (177 kb) | 0.7 (0.6, 0.8) | 1.3E-05 | 0.7 (0.6, 0.8) | 5.0E-05* | 0.8 (0.7, 0.9) | 1.9E-04 |
| 8 | rs7000234 | 81699669 | ZNF704 (4 kb) | 1.7 (1.3, 2.2) | 2.4E-04 | 1.8 (1.4, 2.4) | 6.1E-05* | 1.5 (1.2, 1.9) | 2.2E-04 |
| 20 | rs6075164 | 16985876 | PCSK2 (169 kb) | 0.7 (0.6, 0.8) | 2.8E-06 | 0.8 (0.7, 0.9) | 0.0016 | 0.8 (0.7, 0.9) | 2.7E-04 |
| 4 | rs12651081 | 88103790 | AFF1 | 0.9 (0.7, 1.0) | 0.060 | 0.8 (0.6, 1.0) | 0.10 | 0.8 (0.7, 0.9) | 3.1E-04 |
*
Significant in replication-only analysis after Bonferroni adjustment (p<1.8×10−4).