Table 2.
Breast cancer subgroups identified by genome profiling using different analysis platforms in COSMIC database
| Cancer types | Cases | Top 10 genes |
|---|---|---|
| Acinar cell carcinoma | 20 | TP53 (40%), PIK3CA (24%), GATA3 (15%), KMT2C (7%), PTEN (6%), ESR1 (6%), ERBB2 (5%), ARID1A (5%), AKT1 (4%), NF1 (4%) |
| Adenoid cystic carcinoma | 8 | NOTCH1 (67%), KMT2C (67%), PTEN (40%), BRAF (11%), PIK3CA (11%), TP53 (33%), PIM1(33%), TRAF7 (33%), MYOD1 (33%), CREBBP (33%) |
| Basal (triple-negative) carcinoma | 356 | TP53 (50%), PIK3CA (12%), RB1 (6%), CDKN2A (4%), PTEN (4%), KMT2D (5%), PIK3R1 (3%), ATR (4%), ARID1A (3%), BRAF (2%) |
| Ductal carcinoma | 2645 | TP53(40%), PIK3CA (24%), GATA3(15%), KMT2C (7%), PTEN (6%), ESR1 (6%), ERBB2 (5%), ARID1A (5%) NF1 (4%) |
| Ductolobular carcinoma | 93 | PIK3CA (42%), CDH1 (35%), TP53 (13%), NF1 (11%), ERBB2 (11%), ESR1 (8%), TBX3 (10%), ARID1A (9%), KMT2C (9%), AKT1 (7%) |
| ER-HER2-positive | 15 | TP53 (71%), PIK3Ca (22%), GATA3 (7%), ERBB2 (4%) RB1 (14%), JAK2 (7%), SMAD4 (7%), GNAQ (7%), VHL (7%), ATM (7%) |
| ER-positive carcinoma | 345 | PIK3CA (32%), TP53 (24%), GATA3 (15%), IL6ST (38%), KMT2C (14%), CDH1 (12%), ESR1 (9%), PTEN (9%), BRCA 2(9%), ERBB2 (9%) |
| ER-PR-HER2-Positive | 28 |
PIK3CA (29%), TP53 (29%), CDH1(12%), GATA3 (14%), ERBB2 (14%), PCM1 (14%), CREBBP (14%), RARA (7%), FOXA1 (7%), ATR (7%) |
| ER-PR-positive carcinoma | 334 | PIK3CA (33%), TP53 (22%), GATA3 (17%), ESR1 (10%), CDH1 (9%), KMT2C (10%), AKT1 (7%), SPEN (5%), FAT4 (6%), MAP2K4 (4%) |
| HER2-positive carcinoma | 478 | TP53 (46%), PIK3CA (22%), KMT2D (8%), LRP1B (8%), PREX2 (6%), KMT2C (6%), ERBB2(3%), MEN1(4%), ZFHX3(5%), NCOR2(%2) |
| Lobular carcinoma | 457 | CDH1 (55%), PIK3CA (41%), TP53(19%), ERBB2(17%), KMT2C (16%), TBX3(13%), ESR1(7%), FOXA1(7%), ARID1A(6%) |
| Luminal A carcinoma | 23 |
PIK3CA (48%), RUNX1 (11%), MAP2K4 (7%), TP53 (10%), ASXL1 (4%), EGFR (5%) |
| Luminal B carcinoma | 27 | PIK3CA (28%), TP53 (7%), RUNX1 (5%), MAP2K4 (6%), JAK2 (2%), KRAS (2%), BRAF (2%), IDH1 (2%), GNAS (2%), PTEN (2%) |
| Luminal NS carcinoma | 275 |
TP53 (60%), PIK3CA (56%), GATA3 (44%), CDH1 (42%), MAP2K4 (18%), ATR (16%), RUNX1 (14%), CDKN1B (14%), RB1 (12%), KMT2C (11%) |
| Medullary carcinoma | 38 | TP53 (76%) |
| Metaplastic | 151 |
TP53 (64%), PIK3CA (33%), KMT2C (14%), LRP1B (15%), CDKN2A (11%), PTEN (8%), KMT2D (8%), ARID1A (8%), PIK3R1 (7%), APC (5%) |
| Neuroendocrine | 25 |
EP300 (100%), PIK3CA (15%), TBX3 (19%), OXA1(19%), KMT2C (19%), HRAS (8%), FGFR1 (4%), KDR (6%),CTCF (13%), ARID1A (13%) |
| Normal like carcinoma | 4 | TP53 (100%), RUNX1 (7%), MAP2K4 (5%) |
| Carcinoma not specified (NS) | 6014 | PIK3CA (28%), TP53 (22%), CDH1 (10%), GATA3 (8%), KMT2C (8%), ESR1 (7%), ERBB2 (4%), NCOR1 (4%), SPEN (4%), NF1 (3%) |
| PR-HER2-positive carcinoma | 2 | PIK3CA (50%), NCOR1 (50%), ERBB4 (50%) |
| PR-positive | 2 | SPEN (40%) |
| Small cell carcinoma | 4 | PIK3A (40%) |