Table 3.
Top SNP hits for breast cancer subtype analyses
| Breast Cancer Subtype | Hormone Receptor +/− | Luminal / Basal-like | HER2 +/− |
|---|---|---|---|
| Sample size | 2081/997 | 1613/405 | 1356/344 |
| SNP ID | rs80339298 | rs147821319 | rs116367195 |
| Chromosome:Position* | 1:52244019 | 5:149217038 | 3:15693446 |
| Effect/Other | A/G | A/G | G/A |
| Reference Sequence | NT_032977.10 | NM_001172698 | NM_001195099 |
| OR (95%CI) | 2.11 (1.54, 2.89) | 2.20 (1.52, 3.19) | 2.70 (1.72, 4.24) |
| EAF | 0.02 | 0.04 | 0.97 |
| p-value** | 2.90 × 10−6 | 2.34 × 10−5 | 1.59 × 10−5 |
| FDR p-value*** | 0.16 | 0.37 | 0.84 |
Abbreviations: OR: odds ratio; 95% CI of the OR; EAF: effect allele frequency; FDR: false discovery rate
* Chromosome: position from GRCh37/hg19 Assembly
** Additive genetic model was adjusted for age group (by ~ 10 year intervals), study site, geographic region of residence, DNA source, and ancestry (PCs 5, 6 and 8 - associated with cancer trait, p-value< 0.1)
***Adjustment for multiple comparisons using the False Discovery Rate (FDR) within each subtype analysis