Table 2.

Highlighted cancer gene alterations in mTNBC

PatientAmpaDelbMutatedStructural variantOverexpressed genesUnderexpressed genes
mTNBC1LRP6CTNNA1NF1ERBB4EGF, HSP90AA1, RASGRF1, TFDP1, MDM4, CCNE2, ARCTNNA1, NF1
PIK3CAPTENRB1
PTGS2GSK3B
mTNBC2BRAFTP53BRAF, NRG3, NFKB2, PARP1, NFKBIA, HRAS
MYCERBB4
NOTCH2
TERT
mTNBC3SMAD3PDGFRB, VEGFC, PDGFRA, GLI2, VEGFA
SMAD6
mTNBC4WT1 KLF8TP53WT1, PAK7ZBTB16/PLZF
mTNBC5IQGAP3ERCC2LRP1BIL2, ALK, AKT2, CBLC, CCNE1, MYCNSFN[14-3-3 sigma]
mTNBC6WHSC1L1FBXW7TOP2AERBB4ID2, RPRM, EREGFBXW7, CTNNA1, DKK1
FGFR1CTNNA1FGFR2
mTNBC7NOTCH2TP53NOTCH2, KIT, GHR, TGFB2, MMP9CDKN2A, SFN[14-3-3 sigma]
DNER
mTNBC8ATG5TP53CAMK2D, ATG5, PTGS2, MET, TGFB2, AR, PDGFRA
MDM2
TOP2A
BRD4
CDH5
mTNBC9BRCA2TP53RB1ERCC4, CCNE2, CDK1, MET, SMC1B, ALK, MYCBRCA1, BRCA2
DCLRE1CPTEN
DDB1BRIP1
RIF1
MEI1
mTNBC10KRASTP53KRAS, DNTTID4, SFRP1
CDH5
mTNBC11SMAD3PTENBRCA1cRB1NOTCH3, TERT, CCNE2, NFKB1, MET, RETNFATC2, TRAF3, SFRP1, DTX1, PTEN, PIK3CG
PTCH2RHEB
mTNBC12MYB ARAFTP53ELK1, ARAF, HMGA2, FGFR2, GLI1, SHH, TGFB2, PDGFRB, PDGFRACDKN2A
CDH5
mTNBC13CADM2,TNNI2TP53DLL1, CCNB3, FGFR2, SMAD6SFRP2, PTCH2
ERCC2STAM2
HMMR
mTNBC14FOXM1PTPRMTP53IGFBP3, PRKCG, NRG4, NRG1CDKN2A
RUNX1STAT1
  • aFocal amplification from outlier analysis with log fold-change ≤ or ≥ 2.0 and P value P ≤ 0.05.

  • bFocal homozygous deletion from outlier analysis with log fold-change ≤ or ≥ 2.0 and P value P ≤ 0.05.

  • cGermline mutation detected from outlier analysis with log fold-change ≤ or ≥ 2.0 and P value P ≤ 0.05.