Table 2.
Haplotype analysis of associations of high grade glioma risk with single nucleotide polymorphisms (SNPs) in 9p21 region and RTEL1.
| Cases % | iControls % | Odds ratio a | p-value a | |
|---|---|---|---|---|
| A. UCSF Adult Glioma Study (AGS) and the Cancer Genome Atlas high grade glioma cases (n=692) and AGS and Illumina controls (n=3992) | ||||
| Chromosome 9p21: rs1063192, rs2157719, rs1412829, rs4977756 | ||||
| T-A-T-A | 50.0 | 58.5 | Referent | |
| C-G-C-G | 43.2 | 35.1 | 1.42 (1.26–1.60) | 1.4 × 10−8 |
| Rare haplotypes b | 6.8 | 6.4 | 1.22 (0.96–1.56) | 0.110 |
| Global p-value: 7.4× 10−8a | ||||
| RTEL1: rs4809324, rs6010620, rs6089953 | ||||
| T-G-G | 68.0 | 66.9 | Referent | |
| T-A-A | 16.1 | 21.7 | 0.71 (0.61–0.83) | 1.8 × 10−5 |
| C-G-G | 15.0 | 10.3 | 1.40 (1.18–1.66) | 9.6 × 10−5 |
| Rare haplotypes b | 0.9 | 1.1 | 1.12 (0.57–2.19) | 0.750 |
| Global p-value: 3.6 × 10−9 a | ||||
| B. 176 Mayo Clinic glioblastoma and anaplastic astrocytoma cases and 174 Mayo Clinic general medicine controls. | ||||
| Chromosome 9p21: rs1063192, rs2157719, rs1412829, rs4977756 | ||||
| T-A-T-A | 44.6 | 56.6 | Referent | |
| C-G-C-G | 49.7 | 36.5 | 1.68 (1.23–2.29) | 0.001 |
| Rare haplotypes b | 5.7 | 6.9 | 0.96 (0.50–1.84) | 0.900 |
| Global p-value: 0.002a | ||||
| RTEL1: rs4809324, rs6010620, rs6089953 | ||||
| T-G-G | 68.1 | 63.2 | Referent | |
| T-A-A | 14.8 | 25.0 | 0.52 (0.35–0.79) | 0.002 |
| C-G-G | 16.5 | 10.3 | 1.42 (0.89–2.26) | 0.144 |
| Rare haplotypes b | 0.6 | 1.5 | 0.41 (0.08–2.22) | 0.303 |
| Global p-value: 0.002a | ||||
a
Principal component adjusted odds ratios, confidence intervals and p-values were estimated using Eigenstrat software; SNPs with individual p<10−6 were included in the haplotype analyses.
b
Rare haplotypes (<5%) were grouped together for these analyses.