Table 5.
Associations with ductal and lobular breast cancer a
| N tumors with morphology (MAF) | Other morphology | Tumors with morphology | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Subtype | Sample | SNP | Locus | Position b | Nearby gene | Ref c | Eff d | Reported e | Present | Other | Unknown | Number unaffected (MAF) | HR (95% CI) | P -value | HR (95% CI) | P -value | P het-value f |
| Ductal | BRCA1 carriers | rs10069690 | 5p15.33 | 1332790 | TERT | G | A | Yes | 3,155 (0.29) | 847 (0.30) | 3,783 (0.30) | 7,449 (0.26) | 1.23 (1.11 to 1.36) | 7.3 × 10−5 | 1.20 (1.14 to 1.26) | 2.0 × 10−11 | 0.67 |
| rs11155803 | 6q25.1 | 151987362 | C6orf97 | A | G | Yes | 3,159 (0.36) | 848 (0.35) | 3,786 (0.36) | 7,452 (0.32) | 1.13 (1.03 to 1.25) | 0.01 | 1.17 (1.11 to 1.23) | 4.6 × 10−10 | 0.58 | ||
| rs10252939 | 7q36 | 155587448 | A | G | No | 3,159 (0.28) | 849 (0.33) | 3,789 (0.29) | 7,455 (0.32) | 1.08 (0.98 to 1.19) | 0.14 | 0.87 (0.82 to 0.91) | 1.0 × 10−7 | 2.7 × 10−4 | |||
| rs8100241 | 19p13.11 | 17253894 | ANKLE1 | G | A | Yes | 3,137 (0.48) | 844 (0.49) | 3,777 (0.47) | 7,420 (0.52) | 0.87 (0.79 to 0.95) | 2.8 × 10−3 | 0.84 (0.8 to 0.88) | 1.5 × 10−13 | 0.51 | ||
| BRCA2 carriers | rs2162540 | 10q26 | 123342126 | FGFR2 | A | G | Yes | 1,728 (0.45) | 458 (0.44) | 2,038 (0.44) | 3,783 (0.38) | 1.24 (1.08 to 1.42) | 1.8 × 10−3 | 1.30 (1.21 to 1.39) | 3.1 × 10−14 | 0.55 | |
| rs1362548 | 16q12.1 | 51121452 | TOX3 | C | G | Yes | 1,770 (0.3) | 473 (0.32) | 2,087 (0.31) | 3,881 (0.26) | 1.32 (1.15 to 1.51) | 4.8 × 10−5 | 1.23 (1.15 to 1.32) | 7.3 × 10−9 | 0.36 | ||
| Lobular | BRCA2 carriers | rs2186703 | 11q23.3 | 115265717 | RPL15P15 | A | C | No | 188 (0.07) | 2,055 (0.03) | 2,087 (0.04) | 3,881 (0.03) | 1.09 (0.93 to 1.27) | 0.29 | 2.54 (1.78 to 3.62) | 2.8 × 10−7 | 1.5 × 10−5 |
| rs55998524 | Xp11.23 | 51082075 | NUDT10 | C | G | No | 188 (0.11) | 2,054 (0.05) | 2,086 (0.06) | 3,880 (0.05) | 0.96 (0.83 to 1.1) | 0.54 | 2.42 (1.77 to 3.32) | 3.6 × 10−8 | 7.0 × 10−8 | ||
aCI, Confidence interval; HR, Hazard ratio; MAF, Mean allele frequency. Single-nucleotide polymorphisms (SNPs) associated at P <10−6 with ductal carcinomas and, for BRCA2 mutation carriers, lobular carcinomas are shown. The most strongly associated SNP from each locus is reported. bPosition in build 36. cReference allele. dEffect allele. eVariant located in previously reported breast cancer susceptibility locus. fP-value for the difference in SNP association between ductal breast tumors and non-ductal breast tumors and for lobular breast tumors and non-lobular breast tumors.