Table 1 Highlights of genomic, clinical and proteomic features of subtypes

From: Comprehensive molecular portraits of human breast tumours

Subtype Luminal A Luminal B Basal-like HER2E
ER+/HER2 (%) 87 82 10 20
HER2+ (%) 7 15 2 68
TNBCs (%) 2 1 80 9
TP53 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 amp; 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 Hypermethylated phenotype for subset Hypomethylated
Protein expression High oestrogen signalling; high MYB; RPPA reactive subtypes Less oestrogen signalling; high FOXM1 and MYC; RPPA reactive subtypes High expression of DNA repair proteins, PTEN and INPP4B loss signature (pAKT) High protein and phospho-protein expression of EGFR and HER2
  1. Percentages are based on 466 tumour overlap list. Amp, amplification; mut, mutation.