TABLE 2.
SNP rs356219 in SNCA interacts with rs8111699 in SKT11, rs456998 in FCHSD1, and rs1732170 in GSK3B in modulating PD risk
| Gene | SNP | Bal. acc. CV training | Bal. acc. CV testing | CVC | OR (95% CI) | Association P valuea | Epistatic association P valueb |
|---|---|---|---|---|---|---|---|
| SNCA | rs356219 | 0.5378 | 0.5245 | 7/10 | 1.37 (1.13–1.66) | .306–.307 | .925–.926 |
| STK11 | rs8111699 | 0.5529 | 0.5283 | 5/10 | 1.52 (1.26–1.83) | .214–.215 | .874–.875 |
| GSK3B | rs1732170 | ||||||
| SNCA | rs356219 | 0.5729 | 0.5247 | 5/10 | 1.79 (1.48–2.16) | .300–.301 | .924–.925 |
| STK11 | rs8111699 | ||||||
| GSK3B | rs1732170 | ||||||
| SNCA | rs356219 | 0.6181 | 0.5875 | 10/10 | 2.59 (2.14–3.13) | <.001 | <.001 |
| STK11 | rs8111699 | ||||||
| FCHSD1 | rs456998 | ||||||
| GSK3B | rs1732170 | ||||||
Statistically significant P values are bold. Test of association for SNP combinations with PD risk. N = 898 PD cases and N = 921 unrelated controls. Random seed = 10; CVC = 10. CI, confidence interval; CV, cross-validation; CVC, cross-validation count; OR, odds ratio; SNCA, α-synuclein; SNP, single nucleotide polymorphism.
a
Normal P value.
b
P value of explicit test of epistasis obtained with 1000 permutations.