Table 3. Replication of ten previously reported SCC-associated loci.
|
Stage 1 |
Stage 2 |
Meta-analysis |
Prior GWAS |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Region | Gene | Major/minor | MAF (avg imp r2) | P-values | OR | P-values | OR | P-values | OR | P-values | OR |
| rs12203592 | 6p25.3 | IRF4 | C/T | 0.17 (0.99) | 3.0 × 10-101 | 1.62 | 2.1 × 10-5 | 1.56 | 1.9 × 10-110 | 1.62 | 8.3 × 10-97 | 1.56 |
| rs1805007 | 16q24.3 | MC1R | C/T | 0.07 (1.0) | 5.8 × 10-33 | 1.45 | 9.5 × 10-5 | 1.64 | 1.5 × 10-38 | 1.46 | 1.8 × 10-44 | 1.33 |
| rs6059655 | 20q11.22 | RALY-ASIP | G/A | 0.07 (0.99) | 3.6 × 10-14 | 1.28 | 8.2 × 10-1 | 1.03 | 3.2 × 10-14 | 1.26 | 9.0 × 10-21 | 1.32 |
| rs35407 | 5p13.2 | SLC45A2 | G/A | 0.04 (0.98) | 3.6 × 10-15 | 0.59 | 3.6 × 10-2 | 0.58 | 4.2 × 10-14 | 0.59 | 2.8 × 10-28 | 0.52 |
| rs1126809 | 11q14.3 | TYR | G/A | 0.28 (0.99) | 3.5 × 10-14 | 1.17 | 8.1 × 10-1 | 1.02 | 8.3 × 10-14 | 1.16 | 2.2 × 10-20 | 1.19 |
| rs1800407 | 15q13.1 | OCA2 | C/T | 0.07 (1.0) | 8.0 × 10-9 | 1.21 | 8.9 × 10-1 | 0.98 | 7.7 × 10-9 | 1.20 | 3.3 × 10-9 | 0.88 |
| rs10810657 | 9p22.2 | BNC2, CNTLN | A/T | 0.41 (0.98) | 2.4 × 10-7 | 0.91 | 7.9 × 10-3 | 0.82 | 1.2 × 10-8 | 0.90 | 8.2 × 10-9 | 0.9 |
| rs62246017 | 3p13* | FOXP1 | G/A | 0.33 (0.85) | 3.2 × 10-3 | 1.06 | 9.6 × 10-1 | 1.00 | 4.4 × 10-3 | 1.06 | 1.2 × 10-8 | 1.11 |
| rs6791479 | 3q28* | TPRG1/TP63 | A/T | 0.43 (0.99) | 7.0 × 10-2 | 1.03 | 3.5 × 10-3 | 1.23 | 1.3 × 10-2 | 1.05 | 1.5 × 10-11 | 1.13 |
| rs4455710 | 6p21* | HLA-DQA1 | C/T | — | — | — | — | — | — | — | 1.9 × 10-18 | 1.17 |
Avg imp, average imputation; GWAS, genome-wide association study; MAF, minor allele frequency; OR, odds ratio; SCC, squamous cell carcinoma; SNP, single-nucleotide polymorphism.
Ten loci previously reported as associated with SCC via prior GWAS (P<5 × 10−8) are listed, the first seven of which also reached genome-wide significance in this study. Of the remaining three loci (asterisks), two (3p13 and 3q28) reached nominal significance (P<0.05) in this study. In addition, we report genetic locus, nearest genes, major allele, minor allele, MAF as calculated from stage 1 data, avg imp r2 (a measure of imputation quality) for stage 1 and OR with P-value for each stage, calculated with respect to the minor allele. The right-most two columns list P-value and OR from prior GWAS3 for each locus, relative to the minor allele.