Table 3. Non-synonymous somatic mutations with statistically significantly different frequencies between NBCs (excluding mucinous and lobular carcinomas, n=15), and common forms of ER-positive carcinomas as well as invasive lobular carcinomas from TCGA.
| Gene | IDCs-NE (n=15) |
ER+/HER2- (n=210) |
p value |
Odds ratio (95% CI) |
Lum A (n=179) |
p value |
Odds ratio (95% CI) |
Lum B (n=105) |
p value |
Odds ratio (95% CI) |
ILCs (n=127) |
p value |
Odds ratio (95% CI) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FOXA1 | 3 (20%) | 5 (2%) | 0.01 | 10 (1.881-47) | 4 (2%) | 0.01 | 10.63 (1.897-54.54) | 2 (2%) | 0.01 | 12.35 (1.758-108.3) | 9 (7%) | 0.11 | 3.239 (0.6694-13.43) |
| TBX3 | 3 (20%) | 5 (2%) | 0.01 | 10 (1.881-47) | 4 (2%) | 0.01 | 10.63 (1.897-54.54) | 4 (4%) | 0.04 | 6.151 (1.092-31.71) | 12 (9%) | 0.19 | 2.377 (0.5078-10.36) |
| DCHS2 | 3 (20%) | 4 (2%) | <0.01 | 12.51 (2.234-64.11) | 3 (2%) | <0.01 | 14.17 (2.334-86.47) | 2 (2%) | 0.01 | 12.35 (1.758-108.3) | 2 (1%) | <0.01 | 14.98 (2.136-131.2) |
| PIK3CA | 2 (13%) | 88 (42%) | 0.03 | 0.2144 (0.0338-0.9846) | 85 (47%) | 0.01 | 0.1714 (0.0269-0.7949) | 31 (29%) | 0.23 | 0.3698 (0.0566-1.607) | 66 (48%) | 0.01 | 0.1682 (0.0262-0.7295) |
| HUWE1 | 2 (13%) | 4 (2%) | 0.05 | 7.763 (0.9622-45.91) | 2 (1%) | 0.03 | 13.17 (1.332-130.5) | 4 (4%) | 0.16 | 3.819 (0.4709-22.71) | 2 (1%) | 0.05 | 9.315 (0.94-92.46) |
| SVEP1 | 2 (13%) | 4 (2%) | 0.06 | 7.763 (0.9622-45.91) | 3 (2%) | 0.04 | 8.804 (1.014-61.58) | 3 (3%) | 0.11 | 5.114 (0.5868-35.92) | 3 (2%) | 0.08 | 6.211 (0.7138-43.55) |
| MACF1 | 2 (13%) | 4 (2%) | 0.05 | 7.763 (0.9622-45.91) | 4 (2%) | 0.06 | 6.599 (0.8172-39.06) | 0 (0%) | 0.01 | Inf (2.095-Inf) | 1 (1%) | 0.03 | 18.52 (1.37-565.7) |
| CTCF | 2 (13%) | 6 (3%) | 0.09 | 5.159 (0.6914-27.92) | 8 (4%) | 0.17 | 3.257 (0.4548-16.84) | 1 (1%) | 0.04 | 15.29 (1.13-467.7) | 0 (0%) | 0.01 | Inf (2.536-Inf) |
| CDH1 | 1 (11%) | 6 (3%) | 0.38 | 2.415 (0.1002-18.09) | 4 (2%) | 0.33 | 3.096 (0.1205-25.76) | 2 (2%) | 0.33 | 3.619 (0.1186-48.93) | 80 (63%) | <0.01 | 0.04274 (0.002-0.2785) |
| TP53 | 0 (0%) | 53 (25%) | 0.02 | 0 (0-0.7689) | 23 (13%) | 0.22 | 0 (0-1.888) | 35 (33%) | <0.01 | 0 (0-0.5474) | 10 (8%) | 0.59 | 0 (0-3.991) |
Genes are ordered in decreasing order of mutational frequency in NBCs. Statistical analyses were performed using two-tailed Fisher's exact tests and the confidence intervals for the odds ratio estimated using the minimum likelihood method. In bold, statistically significant p values.
CI, confidence interval; ER, oestrogen receptor; IDCs-NE: invasive ductal carcinomas with neuroendocrine differentiation; ILCs: invasive lobular carcinomas; Inf: infinite; Lum: luminal; N, number; NBCs: neuroendocrine breast carcinomas.