Table 2.
Top genome-wide significant regions and their most likely functional variants from regional meta-analyses of oropharyngeal cancers by HPV16 seropattern status.
| Independent regions | Locus | Variant | Infoa | EA/OAb | Frequency (%) | Meta-analysisc | ||
|---|---|---|---|---|---|---|---|---|
| Controls/Cases | OR (95% CI) | P value | Q_p | |||||
| HPV(+)OPCd | ||||||||
| HLA class I | ||||||||
| Intergenic | rs4713462 | genotyped | A/G | 32.6/21.3 | 0.66 (0.59–0.75) | 4.5 × 10−11 | 0.19 | |
| HLA-B | 1501 | 0.97 | P/A | 5.9/3.0 | 0.44 (0.33–0.58) | 1.13 × 10−8 | 0.20 | |
| 156 -Trp | 0.98 | P/A | 6.1/3.2 | 0.45 (0.34–0.59) | 1.05 × 10−8 | 0.21 | ||
| HLA class II | ||||||||
| Class II haplotype | DRB1*1301-DQA1*0103-DQB1*0603 | P/A | 6.7/2.6 | 0.42 (0.31–0.56) | 7.4 × 10−9 | 0.86 | ||
| HLA-DRB1 | 1301 | 0.99 | P/A | 6.7/2.8 | 0.43 (0.32–0.58) | 1.44 × 10−8 | 0.95 | |
| 71 -Glue | 0.94 | P/A | 14.5/7.9 | 0.56 (0.47–0.68) | 2.8 × 10−9 | 0.30 | ||
| HLA-DQA1 | 0103 | 1 | P/A | 7.8/3.1 | 0.45 (0.34–0.59) | 8.7 × 10−9 | 0.90 | |
| HLA-DQB1 | 0603 | 0.98 | P/A | 7.3/3.1 | 0.45 (0.34–0.60) | 3.1 × 10−8 | 0.35 | |
| HPV(-)OPCf | ||||||||
| 12q23.3 | BTBD11 | rs35189640 | 0.94 | T/C | 2.0/4.7 | 2.73 (1.97–3.79) | 1.1 × 10−9 | 1 |
HLA human leukocyte antigen, OR odds ratio, 95% CI confidence interval, Q_p Cochran’s heterogeneity p value
aImputation INFO (R2) is the average across imputation batches.
bEffect allele/other allele; P stands for presence and A stands for absence for amino acid polymorphisms and HLA alleles.
cRegional meta-analyses Europe and North America.
dNumber of subjects: 1078 HPV(+)OPC and 5256 controls.
eamino acid change due to rs9269942 C/A [Ala (GCG) --> Glu (GAG)].
fNumber of subjects: 565 HPV(−)OPC negative and 5256 controls.