Abbreviation	Meaning
ABCG2	ATP-binding cassette transporter G2
ACACB	Acetyl-CoA carboxylase beta
Akt	Protein kinase B
ALDH1A1	Aldehyde dehydrogenase 1 family member A1
AR	Androgen receptor
AREG	Amphiregulin
ATM	Ataxia telangiectasia mutated
ATP	Adenosine triphosphate
AUC	Area under the curve
AURKA	Aurora kinase A
B-MYB	Myb-related protein B
BC	Breast cancer
BCL2	B-cell lymphoma 2
BCL9	B-cell CLL/lymphoma 9
BIRC2	Baculoviral IAP repeat containing 2
BIRC3	Baculoviral IAP repeat containing 3
BL1	Basal-like 1
BL2	Basal-like 2
BLIA	Basal-like immune activated subtype
BLIS	Basal-like immunosuppressed subtype
BRCA1	Breast cancer gene 1
BRCA2	Breast cancer gene 2
CCL5	Chr. chemokine ligand 5
CCND1	Cyclin D1
CCND2	Cyclin D2
CCND3	Cyclin D3
CD20	Cluster of differentiation 20
CD3	Cluster of differentiation 3
CD37	Cluster of differentiation 37
CD3D	Cluster of differentiation 3 delta subunit
CD4	Cluster of differentiation 4
CD44	Cluster of differentiation 44
CDK4	Cyclin-dependent kinase 4
CDK6	Cyclin-dependent kinase 6
CDKN2A	Cyclin-dependent kinase inhibitor 2A
CEP	cTerminally encoded peptide
CMF	Cyclophosphamide/Methotrexate/Fluorouracil
CNAs	Copy number alterations
cT-stage	Clinical tumor stage
CXCL9	Chemokine (C-X-C motif) ligand 9
CXCR3	C-X-C motif chemokine receptor 3
DCN	DECORIN
DDIT4	DNA-damage-inducible transcript 4
DFS	Disease-free survival
DLDA-30	30 probe diagonal linear discriminant analysis
DRFI	Distant recurrence-free interval
DRFS	Distant relapse-free survival
DSBs	Double strand breaks
DUSP4	Dual specificity phosphatase 4
EFS	Event-free survival
EGFR	Epidermal growth factor receptor
EMT	Epithelial-to-mesenchymal transition
ER	Estrogen receptor
ERBB2	Erb-B2 Receptor Tyrosine Kinase 2
ERK	Extracellular signal-regulated kinase
ESR1	Estrogen receptor alpha
ESR2	Estrogen receptor 2
FLT3	Fms-related receptor tyrosine kinase 3
FOXO3a	Forkhead box O3
GATA3	GATA binding protein 3
GBX2	Gastrulation brain homeobox 2
GFR	Growth factor receptor
GGI	Genomic grade index
HER2	Human epidermal growth factor receptor type 2
HOPX	HOP homeobox
HR	Hormone receptor
ICI	Immune checkpoint inhibition
IGF1R	Insulin-like growth factor 1 receptor
IHC	Immunohistochemistry
IM	Immunomodulatory
IntClust	Integrative cluster
IT-TIL	Intratumor-tumor infiltrating lymphocytes
JAK2	Janus kinase 2
Ki67	Antigen Ki67
KRAS	Kirsten rat sarcoma viral oncogene homolog
KRT16	Keratin 16
LABC	Locally advanced breast cancer
LAR	Luminal androgen receptor
LDHB	Lactate dehydrogenase B
LOX	Lysyl oxidase
M	Mesenchymal
MAPK	Mitogen-activated protein kinase
MCL1	Myeloid cell leukemia 1
MEK	Mitogen-activated protein kinase kinase
MES	Mesenchymal subtype
MKi67	Marker of proliferation Ki-67
MMP28	Matrix metallopeptidase 28
MSL	Mesenchymal stem-like
mTOR	Mechanistic target of rapamycin kinase
MUC1	Mucin 1, cell surface associated
MYC	Master regulator of cell cycle entry and proliferative metabolism
NAC	Neoadjuvant chemotherapy
OR	Odds ratio
OS	Overall survival
PAM50	Prediction analysis of microarray 50 subtypes
PARP	Poly ADP-ribose polymerase
PARPi	PARP inhibitor
PAWR	Pro-apoptotic WT1 regulator
pCR	Pathological complete response
PD-1	Programmed D-1
PD-L1	Programmed D ligase-1
PDGF	Platelet-derived growth factor
PI	Prognostic index
PI3K	Phosphatidylinositol 3-kinase
PI3KCA	Phosphatidylinositol 3-kinase catalytic subunit alpha
PLAU	Plasminogen activator, urokinase
POLR1C	RNA polymerase I And III Subunit C
PR	Progesterone receptor
PTEN	Phosphatase and tensin homolog
QCCs	Quiescent cancer cells
RB1	Retinoblastoma protein 1
RCB	Residual cancer burden
RD	Residual disease
RFS	Relapse-free survival
RhoA	Ras homolog family member A
RPCB	Residual proliferative cancer burden
SMAD4	SMAD family member 4
SNAI1	Snail family transcriptional repressor 1
SNAI2	Snail family transcriptional repressor 2
SOX9	SRY-box transcription factor 9
SPAG5	Sperm-associated antigen 5
SPARC	Secreted protein acidic and cysteine-rich
SSBs	Single strand breaks
STAT	Signal transducer and activator of transcription
STAT1	Signal transducer and activator of transcription 1
STAT3	Signal transducer and activator of transcription 3
Str-TIL	Stromal-tumor infiltrating lymphocytes
TCGA	The Cancer Genome Atlas
TGFa	Transforming growth factor alpha
TGFb	Transforming growth factor beta
TILs	Tumor infiltrating lymphocytes
TN	Triple negative
TOP2A	Topoisomerase IIA
TP53	Tumor protein 53
TRAR	Trastuzumab risk model signature
TWIST	Twist basic helix-loop-helix transcription factor
VTCN1	V-set domain containing T cell activation inhibitor 1
WNT11	Wnt family member 11
WNT5A	Wnt family member 5A