Table 2.
Results combining primary family-based and replication case–control studies in the conditional logistic regression framework
| SNP | Closest geneb | Locationc | M | M | MAF founders |
MAF cases | MAF controls |
Model | Discovery | Replication | Full sample
|
Age < 25 yearsa
|
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| pd | pd | OR (95 % CI)d | pd | OR (95 % CI)d | pd | |||||||||
| rs916943 | AGMO | 7 : 15593768 Intron 2 | T | C | 0.08 | 0.08 | 0.05 | ADD | 2.7 × 10−6 | 0.009 | 1.86 (1.33, 2.6) | 0.0002 | 2.73 (1.78, 4.18) | 2.0 × 10−6 |
| rs358793 | WNT5A | 3: 55361433 138.3 kb downstream | T | C | 0.49 | 0.48 | 0.57 | ADD | 9.7 × 10−5 | 0.0004 | 0.68 (0.57, 0.82) | 4.0 × 10−5 | 0.69 (0.53, 0.90) | 0.0057 |
| rs17590261 | PCDH10 | 4: 136564124 2.49 Mb upstream | C | T | 0.1 | 0.14 | 0.11 | REC | 3.5 × 10−5 | 0.003 | 6.24 (2.38, 16.33) | 2.2 × 10−5 | 5.47 (1.66, 18.05) | 0.0023 |
| rs6786408 | FOXP1 | 3: 71263218 Intron 5 | A | C | 0.48 | 0.54 | 0.45 | ADD | 2.8 × 10−5 | 0.0007 | 1.47 (1.23, 1.79) | 1.9 × 10−5 | 1.67 (1.28, 2.13) | 8.2 × 10−5 |
M major allele, m minor allele, MAF minor allele frequency
a
The number of affected individuals included in this analysis are 277 affected offspring and cases <25 years (or 50% of the total affected offspring and cases used in the full sample)
b
Gene in which the SNP is located, or closest gene
c
Chromosome with location in base pairs, and gene position or distance from the closest gene
d
Two-sided test based on the minor allele among founders