Table 2.
Prevalence of genomic alterations in primary tumors of patients initially diagnosed with stage I-III breast cancer versus treatment-naïve primary tumors of patients diagnosed with de novo metastatic breast cancer (dnMBC). Alterations include gene mutations (without OncoKB filtering), gene copy number variations (high amplification or deep deletion) and chromosome arm level changes. Displayed here are genes/chromosome arms with unadjusted p values < 0.05 and other genes of interest; highlighted in blue are genes with adjusted q values < 0.25. Numbers of samples available for each comparison are displayed. Comparison of median TMB (mutations/megabase) is also included (Wilcoxon, significant p < 0.05).
| SUBTYPE AND ALTERATIONS | Primary tumors in Stage I-III | Primary tumors in dnMBC | Unadjusted p value | FDR q value | Odds Ratio | ||
|---|---|---|---|---|---|---|---|
| HR+/HER2− | |||||||
| MUTATION | (n=235) | (n=89) | |||||
| N | % | N | % | ||||
| BRCA1 | 18 | 7.7 | 0 | 0 | 0.005 | 1 | Inf |
| SETD2 | 5 | 2.1 | 8 | 9.0 | 0.009 | 1 | 0.2 |
| KMT2D | 14 | 6.0 | 13 | 14.6 | 0.022 | 1 | 0.4 |
| CDKN1B | 4 | 1.7 | 6 | 6.7 | 0.029 | 1 | 0.2 |
| HNF1A | 3 | 1.3 | 5 | 5.6 | 0.039 | 1 | 0.2 |
| BRD4 | 3 | 1.3 | 5 | 5.6 | 0.039 | 1 | 0.2 |
| TP53 | 76 | 32.3 | 19 | 21.3 | 0.056 | 1 | 1.8 |
| TMB (median) | 7.220 | 7.220 | 0.167 | ||||
| CHROMOSOME ARM | (n=106) | (n=41) | |||||
| N | % | N | % | ||||
| 5p gain | 12 | 11.3 | 11 | 26.8 | 0.040 | 0.980 | 0.4 |
| 20q gain | 27 | 25.5 | 4 | 9.8 | 0.043 | 0.980 | 3.1 |
| HR+/HER2+ | |||||||
| MUTATION | (n=36) | (n=24) | |||||
| N | % | N | % | ||||
| NOTCH1 | 0 | 0 | 3 | 12.5 | 0.059 | 1 | 0 |
| TMB (median) | 6.618 | 7.220 | 0.581 | ||||
| CHROMOSOME ARM | (n=16) | (n=13) | |||||
| N | % | N | % | ||||
| 15q gain | 0 | 0 | 4 | 30.8 | 0.030 | 0.980 | 0 |
| 16q loss | 7 | 43.8 | 1 | 7.7 | 0.044 | 1 | 8.7 |
| HR-/HER2+ | |||||||
| MUTATION | (n=22) | (n=13) | |||||
| N | % | N | % | ||||
| IKZF3 | 0 | 0 | 3 | 23.1 | 0.044 | 1 | 0 |
| ARID1B | 1 | 4.5 | 4 | 30.8 | 0.052 | 1 | 0.1 |
| TMB (median) | 7.822 | 6.598 | 0.129 | ||||
| ALL HER2+ | |||||||
| MUTATION | (n=58) | (n=37) | |||||
| N | % | N | % | ||||
| CDC73 | 0 | 0 | 3 | 8.1 | 0.056 | 1 | 0 |
| EPHA5 | 0 | 0 | 3 | 8.1 | 0.056 | 1 | 0 |
| IKZF3 | 0 | 0 | 3 | 8.1 | 0.056 | 1 | 0 |
| MTOR | 0 | 0 | 3 | 8.1 | 0.056 | 1 | 0 |
| TMB (median) | 7.220 | 7.220 | 0.824 | ||||
| CHROMOSOME ARM | (n=26) | (n=21) | |||||
| N | % | N | % | ||||
| 16q loss | 12 | 46.2 | 3 | 14.3 | 0.029 | 1 | 5.0 |
| 15q gain | 0 | 0 | 4 | 19.0 | 0.034 | 0.980 | 0 |
| 7p gain | 0 | 0 | 4 | 19.0 | 0.034 | 0.980 | 0 |
| TNBC | |||||||
| MUTATION | (n=101) | (n=19) | |||||
| N | % | N | % | ||||
| CIITA | 1 | 1.0 | 5 | 26.3 | 3.3E-04 | 0.233 | 0.03 |
| TMB (median) | 7.220 | 7.220 | 0.846 | ||||
| HIGH GENE AMPLIFICATION | (n=101) | (n=19) | |||||
| N | % | N | % | ||||
| MYB | 0 | 0 | 4 | 21.1 | 4.7E-04 | 0.111 | 0 |
| CHROMOSOME ARM | (n=45) | (n=9) | |||||
| N | % | N | % | ||||
| 5p loss | 8 | 17.8 | 5 | 55.6 | 0.028 | 1 | 0.2 |