Patent ID: 8868352

Claim:
A method for predicting the likelihood of a beneficial response to treatment with chemotherapy of a human patient diagnosed with breast cancer, comprising (a) measuring a level of an RNA transcript of each of the genes BIRC5, MKi67, MYBL2, CCNB1, STK6, MMP11, SCUBE2, ERBB2, GRB7, ESR1, PGR, BCL2, CTSL2, GSTM1, CD68, and BAG1, in a biological sample comprising a breast tumor sample obtained from said human patient, (b) normalizing the level of the RNA transcript of each of the genes the at least one gene to obtain a normalized gene expression level for each gene, (c) determining the values of the following variables: (i) Recurrence Score; (ii) ESR1 Group Score; (iii) Invasion Group Score; and (iv) Proliferation Group Threshold Score and, (d) predicting the likelihood of a beneficial response to treatment with chemotherapy of the patient based on the values of the variables of step (c), (e1) for every unit of an increase in the value of one or more of (i), (iii), or (iv), said human patient is identified to have a proportionately increased likelihood of a beneficial response to said treatment; and (e2) for every unit of an increase in the value of (ii), said subject is identified to have a proportionately decreased likelihood of a beneficial response to said treatment; and (e3) for every unit of an increase in the value of (i), said human patient is identified as having an increased likelihood of a beneficial response to said treatment, as measured by a reduced risk of breast cancer recurrence; wherein ESR1 Group Score=(ESR1+PGR+BCL2+SCUBE2)/4; Invasion Group Score=(CTSL2+MMP11)/2; Proliferation Group Threshold Score equals 6.5, if a Proliferation Group Score is less than 6.5; and the Proliferation Group Threshold Score equals a Proliferation Group Score, if the Proliferation Group Score is 6.5 or more; wherein the Proliferation Group Score=(BIRC5+MKI67+MYBL2+CCNB1+STK6)/5; and Recurrence ⁢ ⁢ Score ⁢ ⁢ RS = { 0 if ⁢ ⁢ 20 × ( RS U - 6.7 ) < 0 20 × ( RS U - 6.7 ) if ⁢ ⁢ 0 ≤ 20 × ( RS U - 6.7 ) ≤ 100 100 if ⁢ ⁢ 20 × ( RS U - 6.7 ) > 100 wherein RSu (Recurrence Score unscaled)= 0.47×GRB7 Group Threshold Score −0.34×ESR1 Group Score +1.04× Proliferation Group Threshold Score +0.10× Invasion Group Score +0.05×CD68 −0.08×GSTM1 −0.07×BAG1 wherein the GRB7 Group Threshold Score equals 8, if a GRB7 Group Score is less than 8; and the GRB7 Group Threshold Score equals a GRB7 Group Score, if the GRB7 Group Score is 8 or more; wherein the GRB7 Group Score=0.9×GRB7+0.1×ERBB2; where the gene symbols in the equations represent the normalized expression levels of the RNA transcripts of the respective genes.