Table 2.
Most frequently mutated breast cancer-associated genes in breast cancers derived from PHTS and TCGA
| Genes | PHTS |
TCGA |
||||||
|---|---|---|---|---|---|---|---|---|
| All cases (n = 44) no. (%) |
TIER-1 (n = 31) no. (%) |
TIER-2 (n = 13) no. (%) |
All cases (n = 497) no. (%) |
ER+/HER2− (n = 308) no. (%) |
ER+/HER2+ (n = 80) no. (%) |
ER−/HER2+ (n = 23) no. (%) |
TNBC (n = 86) no. (%) |
|
| PTEN | 10 (22.7) | 9 (29.0) | 1 (7.7) | 28 (5.6) | 17 (5.5) | 5 (6.3) | 0 (0) | 6 (7.0) |
| PIK3CA | 10 (22.7) | 4 (12.9) | 6 (46.2) | 166 (33.4) | 125 (40.6) | 29 (36.3) | 2 (8.7) | 10 (11.6) |
| MAP3K1 | 6 (13.6) | 3 (9.7) | 3 (23.1) | 45 (9.1) | 32 (10.4) | 8 (10.0) | 3 (13.0) | 2 (2.3) |
| TP53 | 5 (11.4) | 4 (12.9) | 1 (7.7) | 171 (34.4) | 62 (20.1) | 21 (26.3) | 17 (73.9) | 71 (82.6) |
| GATA3 | 4 (9.1) | 4 (12.9) | 0 (0) | 56 (11.3) | 48 (15.6) | 8 (10.0) | 0 (0) | 0 (0) |
| TBX3 | 4 (9.1) | 1 (3.2) | 3 (23.1) | 22 (4.4) | 19 (6.2) | 1 (1.3) | 0 (0) | 2 (2.3) |
| AFF2 | 3 (6.8) | 3 (9.7) | 0 (0) | 10 (2.0) | 3 (1.0) | 4 (5.0) | 1 (4.4) | 2 (2.3) |
| ATM | 3 (6.8) | 2 (6.5) | 1 (7.7) | 9 (1.8) | 5 (1.6) | 2 (2.5) | 0 (0) | 2 (2.3) |
| CBFB | 3 (6.8) | 3 (9.7) | 0 (0) | 9 (1.8) | 7 (2.3) | 2 (2.5) | 0 (0) | 0 (0) |
| KMT2C | 2 (4.5) | 1 (3.2) | 1 (7.7) | 51 (10.3) | 38 (12.3) | 8 (10.0) | 0 (0) | 5 (5.8) |
| NF1 | 2 (4.5) | 2 (6.5) | 0 (0) | 16 (3.2) | 10 (3.3) | 3 (3.8) | 0 (0) | 3 (3.5) |
| RB1 | 2 (4.5) | 1 (3.2) | 1 (7.7) | 15 (3.0) | 3 (1.0) | 3 (3.8) | 0 (0) | 9 (10.5) |
| RUNX1 | 2 (4.5) | 1 (3.2) | 1 (7.7) | 21 (4.2) | 14 (4.6) | 5 (6.3) | 0 (0) | 2 (2.3) |
| AR | 2 (4.5) | 2 (6.5) | 0 (0) | 4 (0.8) | 3 (1.0) | 1 (1.3) | 0 (0) | 0 (0) |
| FANCC | 2 (4.5) | 2 (6.5) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
Abbreviations: PHTS, PTEN hamartoma tumor syndrome (germline PTEN variant positive); TCGA, The Cancer Genome Atlas; TIER-1, breast cancers arising from germline PTEN variants classified as pathogenic or likely pathogenic; TIER-2, breast cancers arising from germline PTEN variants classified as variants of unknown significance or likely pathogenic; ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; TNBC, triple negative breast cancer.
The table shows a comparison of the most frequently mutated BC-associated genes between PHTS (all cases combined), TIER-1, TIER-2, and TCGA sporadic breast cancer groups. The genes are listed in descending order by the percentage of samples harboring somatic variants (single-nucleotide variants and indels) in each gene.