Table 2.
Associations of TGCT with replicated SNP markers
| Gene | Markera | Risk allele | Genotype Countb | Phase | Per allele | OR (95% CI) Heterozygotec | Homozygoted | P-trende | |
|---|---|---|---|---|---|---|---|---|---|
| Controls | Cases | ||||||||
| KITLG | rs3782179 A/G | A | 597/276/44 | 229/45/3 | Discovery | 2.36 (1.73, 3.21) | 2.39 (0.71, 8.03) | 5.63 (1.73, 18.3) | 1.95 × 10−8 |
|
| |||||||||
| 515/285/38 | 309/49/5 | Replication | 3.08 (2.29, 4.13) | 1.31 (0.49, 3.48) | 4.56 (1.78, 11.7) | 5.88 × 10−15 | |||
|
| |||||||||
| rs4474514 A/G | A | 599/276/44 | 229/45/2 | Discovery | 2.45(1.79,3.35) | 3.59(0.84, 15.3) | 8.41 (2.02, 35.0) | 7.34 × 10−9 | |
|
| |||||||||
| 517/285/38 | 310/49/5 | Replication | 3.07 (2.29, 4.13) | 1.31 (0.49, 3.48) | 4.56 (1.77, 11.7) | 5.88 × 10−15 | |||
|
| |||||||||
| SPRY4 | rs4324715 T/C | T | 230/433/255 | 87/145/33 | Discovery | 1.59 (1.30, 1.93) | 2.59 (1.72, 3.89) | 2.92 (1.89, 4.53) | 3.57 × 10−6 |
|
| |||||||||
| 191/437/197 | 119/171/68 | Replication | 1.37 (1.14, 1.64) | 1.13 (0.82, 1.57) | 1.81 (1.26, 2.58) | 6.77 × 10−4 | |||
|
| |||||||||
| rs6897876 C/T | C | 282/429/207 | 114/135/28 | Discovery | 1.59 (1.31, 1.94) | 2.33 (1.50, 3.61) | 2.99 (1.90, 4.69) | 2.96 × 10−6 | |
|
| |||||||||
| 251/428/154 | 156/149/57 | Replication | 1.39 (1.16, 1.66) | 0.94 (0.66, 1.34) | 1.68 (1.17, 2.42) | 3.67 × 10−4 | |||
a
dbSNP rsnumber and major/minor alleles.
b
Number of individuals genotyped as homozygous for the risk allele/heterozygous for the risk allele/homozygous for the non-risk allele. Nomenclature for major/minor alleles based on calls from Affymetrix® Genome-Wide Human SNP Array 6.0. MAF for discovery phase markers given in Supplemental Table 1.
c
OR for heterozygous carriage of risk allele compared to homozygous carriage of non-risk allele.
d
OR for homozygous carriage of risk allele compared to homozygous carriage of non-risk allele.
e
Cochran-Armitage test for trend.