Table 1.
Summary of disease subtypes findings highlighting some of the dominant genomic, clinical, and proteomic features.
| Luminal A | Luminal B | Basal-like | HER2E | |
|---|---|---|---|---|
| % ER+/HER2− | 87% | 82% | 10% | 20% |
| % HER2+ | 7% | 15% | 2% | 68% |
| % TNBC | 2% | 1% | 80% | 9% |
| p53 Pathway | TP53 mut (12%) Gain of MDM2 (14%) |
TP53 mut (32%) Gain of MDM2 (31%) |
TP53 mut (84%) Gain of MDM2 (14%) |
TP53 mut (75%) Gain of MDM2 (30%) |
| PIK3CA/PTEN Pathway | PIK3CA mut (49%) PTEN mut/loss (13%) INPP4B loss (9%) |
PIK3CA mut (32%) PTEN mut/loss (24%) INPP4B loss (16%) |
PIK3CA mut (7%) PTEN mut/loss (35%) INPP4B loss (30%) |
PIK3CA mut (42%) PTEN mut/loss (19%) INPP4B loss (30%) |
| RB1 Pathway | Cyclin D1 amp (29%) CDK4 gain (14%) Low expression of CDKN2C High expression of RB1 |
Cyclin D1 amp (58%) CDK4 gain (25%) |
RB1 mut/loss (20%) Cyclin E1 amp (9%) High expression of CDKN2A Low expression of RB1 |
Cyclin D1 amp (38%) CDK4 gain (24%) |
| mRNA Expression | High ER cluster Low proliferation |
Lower ER cluster High proliferation |
Basal signature High proliferation |
HER2 amplicon signature High proliferation |
| Copy Number | Most diploid Many with quiet genomes 1q, 8q, 8p11 gain 8p, 16q loss 11q13.3 amp (24%) |
Most aneuploid Many with focal amps 1q, 8q, 8p11 gain 8p, 16q loss 11q13.3 amp (51%) 8p11.23 amp (28%) |
Most aneuploid High genomic instability 1q, 10p gain 8p, 5q loss MYC focal gain (40%) |
Most aneuploid High genomic instability 1q, 8q gain 8p loss 17q12 focal ERRB2 amp (71%) |
| DNA Mutations | PIK3CA (49%) TP53 (12%) GATA3 (14%) MAP3K1 (14%) |
TP53 (32%) PIK3CA (32%) MAP3K1 (5%) |
TP53 (84%) PIK3CA (7%) |
TP53 (75%) PIK3CA (42%) PIK3R1 (8%) |
| DNA Methylation | Hyper-methylated phenotype for subset | Hypo-methylated | ||
| Protein Expression | High Estrogen-signaling High cMYB RPPA reactive subtypes |
Less Estrogen-signaling High FOXM1 and cMYC RPPA reactive subtypes |
High expression of DNA repair proteins, PTEN and INPP4B loss signature (p-AKT) | High protein and phos-protein expression of HER1 and HER2 |
Percentages are based on 466 tumor overlap list