Methods and kits comprising gene signatures for stratifying breast cancer patients

1. A method for treating a human subject having a ER+/HER2− breast cancer comprising steps of:

(a) determining, in a breast tissue or breast cell sample from the subject the expression of group of genes;

(b) calculating a risk score based upon the expression of the group of genes, wherein a higher risk score indicates an increased risk of breast cancer recurrence in the subject,

wherein the risk score is calculated according to the following formula:

Risk score=Σ i (β i *Cq normalized ),

wherein Cq normalized is calculated according to the following formula:

Cq normalized =AVG Cq−SF,

wherein SF is the difference between the AVG Cq value of at least one reference gene for each subject and a constant reference value K, wherein K=25.012586069, which represents the mean of the AVG Cq of the at least one reference gene calculated across a plurality of training samples;

(c) stratifying the subject into a high or low risk group; and

(d) administering a breast cancer treatment to the subject, wherein a subject stratified in a high risk group is provided a cancer treatment that is more aggressive than the cancer treatment provided to a subject stratified in a low risk group;

wherein said group of genes consists of:

(i) EIF4EBP1, MRPS23, and TOP2A;

(ii) APOBEC3B, CENPW, EIF4EBP1, EXOSC4, LY6E, MMP1, MRPS23, NDUFB10, and TOP2A;

(iii) ALYREF, APOBEC3B, CDK1, CENPW, EIF4EBP1, EXOSC4, H2AFJ, LY6E, MIEN1, MMP1, MRPS23, NDUFB10, NOL3, RACGAP1, SFN, and TOP2A; or

(iv) H2AFZ, CDK1, EXOSC4, PHLDA2, APOBEC3B, EIF4EBP1, SFN, PHB, EPB41L5, RACGAP1, MRPS23, TOP2A, H2AFJ, NOL3, MIEN1, CENPW, LY6E, ALYREF, MMP1, and NDUFB10.

2. The method of claim 1 , wherein the at least one reference gene is selected from the group consisting of GAPDH, GUSB, HPRT1, and TBP.

3. The method of claim 1 , wherein the gene expression is determined using reverse transcription and real-time quantitative polymerase chain reaction (RT-qPCR) with primers and/or probes specific for each gene of the said group of genes.

4. The method of claim 1 , wherein the sample is a breast tumor obtained from the subject, a cancerous breast cell obtained from the subject, or a breast cancer stem cell obtained from the subject.

5. The method of claim 1 , wherein the breast cancer treatment comprises surgery, radiation, anthracycline agents, alkylating agents, nucleoside analogs, platinum agents, vinca agents, anti-estrogen drugs, aromatase inhibitors, ovarian suppression agents, endocrine/hormonal agents, bisphophonate therapy agents, targeted biological therapy agents, and antibodies, or combinations thereof.

6. The method of claim 5 , wherein the breast cancer treatment comprises cyclophosphamide, fluorouracil, 5-fluorouracil, methotrexate, thiotepa, carboplatin, cisplatin, gemcitabine, anthracycline, taxanes, paclitaxel, protein-bound paclitaxel, doxorubicin, docetaxel, vinorelbine, tamoxifen, raloxifene, toremifene, fulvestrant, irinotecan, ixabepilone, temozolmide, topotecan, vincristine, vinblastine, eribulin, mutamycin, capecitabine, capecitabine, anastrozole, exemestane, letrozole, leuprolide, abarelix, buserlin, goserelin, megestrol acetate, risedronate, pamidronate, ibandronate, alendronate, denosumab, zoledronate, trastuzumab, tykerb or bevacizumab, or combinations thereof.