Table 3. Associations between SNPs and subtype-specific ovarian cancer risk in discovery and replication stages.
| Subtype(s) | SNP (Maj>Min) | Location | MAF | Sample description | # Cases | # Controls | OR (95% CI)a | P | Phet |
|---|---|---|---|---|---|---|---|---|---|
| Mucinous | rs11108890 C>A | Chr12:96137530 | 0.04 | Discovery | 78 | 392 | 3.05 (1.32-7.06) | 0.0091 | |
| Replication | 1483 | 21530 | 1.33 (1.11-1.61) | 0.0026 | 0.42 | ||||
| Rep+OVA | 1578 | 22278 | 1.38 (1.16-1.66) | 0.0004 | 0.38 | ||||
|
| |||||||||
| rs933518 G>A | Chr16: 53079622 | 0.08 | Discovery | 78 | 392 | 2.29 (1.32-4.00) | 0.0034 | ||
| Replication | 1483 | 21530 | 1.20 (1.04-1.38) | 0.0141 | 0.81 | ||||
| Rep+OVA | 1578 | 22278 | 1.26 (1.11-1.45) | 0.0008 | 0.41 | ||||
|
| |||||||||
| rs17106154 A>G | Chr14: 68230927 | 0.07 | Discovery | 78 | 392 | 1.78 (0.95-3.37) | 0.0738 | ||
| Replication | 1483 | 21530 | 1.17 (1.02-1.35) | 0.0287 | 0.96 | ||||
| Rep+OVA | 1578 | 22278 | 1.21 (1.06-1.39) | 0.0058 | 0.83 | ||||
|
| |||||||||
| rs970651 G>A | Chr13: 47351705 | 0.16 | Discovery | 78 | 392 | 2.54 (1.54-4.19) | 0.0003 | ||
| Replication | 1483 | 21530 | 1.12 (1.01-1.24) | 0.0334 | 0.81 | ||||
| Rep+OVA | 1578 | 22278 | 1.16 (1.05-1.28) | 0.0042 | 0.44 | ||||
|
| |||||||||
| rs7981902 A>G | Chr13: 47368792 | 0.13 | Discovery | 78 | 392 | 2.26 (1.32-3.86) | 0.0029 | ||
| Replication | 1483 | 21530 | 1.13 (1.01-1.27) | 0.0308 | 0.94 | ||||
| Rep+OVA | 1578 | 22278 | 1.15 (1.03-1.28) | 0.0114 | 0.84 | ||||
|
| |||||||||
| Endometrioid/Clear Cell | rs2190503 G>A | Chr7: 50710111 | 0.13 | Discovery | 114 | 392 | 1.85 (1.21-2.85) | 0.0049 | |
| Replication | 2903 | 21528 | 1.11 (1.02-1.21) | 0.0137 | 0.12 | ||||
| Rep+OVA | 3060 | 22276 | 1.12 (1.04-1.22) | 0.0050 | 0.11 | ||||
|
| |||||||||
| rs6593140 A>G | Chr7: 50765627 | 0.12 | Discovery | 114 | 392 | 2.03 (1.30-3.17) | 0.0018 | ||
| Replication | 2903 | 21528 | 1.11 (1.02-1.21) | 0.0195 | 0.28 | ||||
| Rep+OVA | 3060 | 22276 | 1.09 (1.03-1.17) | 0.0060 | 0.46 | ||||
|
| |||||||||
| rs2329554 G>A | Chr7: 50842524 | 0.22 | Discovery | 114 | 392 | 1.91 (1.33-2.74) | 0.0004 | ||
| Replication | 2903 | 21528 | 1.08 (1.01-1.16) | 0.0195 | 0.59 | ||||
| Rep+OVA | 3060 | 22276 | 1.12 (1.03-1.22) | 0.0060 | 0.25 | ||||
|
| |||||||||
| LMP Serous | rs9609538 A>G | Chr22: 31139832 | 0.24 | Discovery | 68 | 392 | 0.48 (0.30-0.77) | 0.0023 | |
| Replication | 892 | 21529 | 0.86 (0.77-0.95) | 0.0043 | 1.00 | ||||
| Rep+OVA | 970 | 22277 | 0.84 (0.76-0.93) | 0.0007 | 0.99 | ||||
Abbreviations used: SNP, single nucleotide polymorphism; MAF, minor allele frequency; OR, odds ratio; CI, confidence interval. Within subtype, table is ordered by replication sample P-value. SNP location given for human genome build NBCI36.3. MAF is based on all European controls in OCAC and genotyped as part of COGS. Discovery samples are OVA samples used in the pool-based GWAS and subsequently genotyped by COGS (28 samples with insufficient DNA were not genotyped; hence, the number of cases and controls in pools may be smaller than in Table 1). Replication samples are from OCAC studies participating in COGS, excluding all OVA samples. Rep+OVA includes OCAC studies participating in COGS and all OVA samples.
Discovery sample OR and P-value are from logistic regression assuming an additive genetic model, implemented in PLINK (v1.07). Replication sample OR and P-value are from fixed effects meta-analysis carried out using the rmeta library implemented in the R project, excluding the OVA site. Rep+OVA sample OR and P-value are from fixed effects meta-analysis carried out using the rmeta library implemented in the R project, including the OVA site. Phet is the P-value for Cochran's-Q measure of between study heterogeneity, generated in rmeta. All values are based on individual genotyping data.