Skip to main content

Table 1 Summary of genomics studies

From: The genomic map of breast cancer: which roads lead to better targeted therapies?

Reference Cohort Methods of analysis Summary of key findings
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
  1. CGH, comparative genomic hybridization; ER, estrogen receptor; ES, exome sequencing; MA, microarray; MIRS, microRNA-sequencing; MRS, mutation recurrence screening; RPPA, reverse-phase proteomic array; RS, RNA sequencing; WGS, whole-genome sequencing.