Table 1 Summary of genomics studies

Ellis et al. [8]

Biopsies from ER+ breast tumors undergoing neoadjuvant aromatase inhibitor therapy

WGS (n = 46), ES (n = 31), and MRS (n = 240)

Recurrent mutations in MAP3K1 pathway in ER+ disease with good prognosis; anti-proliferative response to aromatase inhibitor associated with mutational activation of FYN, MAPK, and MYC pathways; recurrent mutations in methyl and demethyltransferases and AT-rich interactive domain-containing genes; ERBB2 mutations in non-ERBB2-amplified breast cancer

Shah et al. [7]

Triple-negative breast cancer cases

WGS (n = 15), ES (n = 54), CGH (n = 104), and RS (n = 80)

Clonal dominance of PIK3CA, PTEN, and TP53 mutations; intragenic PARK2 deletions in TNBC; 30%-40% of somatic mutations are detectable at the RNA level.

Curtis et al. [9]

Unselected primary breast tumors

CGH (n = 1,992) and MA (n = 1,992)

Copy-number alterations influence gene expression in over 40% of the breast cancer genome; deletions in PPP2R2A, MTAP, and MAP2K4; integrated copy-number and microarray data defined 10 unique clusters of breast cancer.

Banerji et al. [10]

Unselected primary breast tumors

WGS (22) and ES (103)

Recurrent mutations in CBFB and RUNX1; recurrent MAGI3-AKT3 fusions which are sensitive in vitro to AKT ATP-competitive inhibitors

Stephens et al. [6]

Unselected primary breast tumors

ES (n = 100)

Novel recurrent mutations in AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1, and TBX3

The Cancer Genome Atlas [11]

Unselected primary breast tumors

MA (n = 547), DNA-methylation array (n = 802), CGH (n = 773), MIRS (n = 697), RPPA

(n = 403), and ES (n = 507)

Luminal breast cancer is most heterogeneously mutated subtype; basal-like breast cancer molecularly resembles serous ovarian carcinoma; mutation patterns consistent with the other studies; convergence of genetic and epigenetic alterations into four primary subtypes of breast cancer