Comparison of efficacy of 95-gene and 21-gene classifier (Oncotype DX) for prediction of recurrence in ER-positive and node-negative breast cancer patients

We recently developed a 95-gene classifier (95 GC ) for the prognostic prediction for ER-positive and node-negative breast cancer patients treated with only adjuvant hormonal therapy. The aim of this study was to validate the efficacy of 95 GC and compare it with that of 21 GC (Oncotype DX) as well as to evaluate the combination of 95 GC and 21 GC . DNA microarray data (gene expression) of ER-positive and node-negative breast cancer patients ( n = 459) treated with adjuvant hormone therapy alone as well as those of ER-positive breast cancer patients treated with neoadjuvant chemotherapy ( n = 359) were classified with 95 GC and 21 GC (Recurrence Online at http://www.recurrenceonline.com/ ). 95 GC classified the 459 patients into low-risk ( n = 285; 10 year relapse-free survival: 88.8 %) and high-risk groups ( n = 174; 70.6 %) ( P = 5.5e−10), and 21 GC into low-risk group ( n = 286; 89.3 %), intermediate-risk ( n = 81; 75.7 %), and high-risk ( n = 92; 64.7 %) groups ( P = 2.9e−10). The combination of 95 GC and 21 GC classified them into low-risk ( n = 324; 88.9 %) and high-risk ( n = 135; 65.0 %) groups ( P = 5.9e−14), and also showed that pathological complete response rates were significantly ( P = 2.5e−6) higher for the high-risk (17.9 %) than the low-risk group (3.6 %). In addition, we demonstrated that 95 GC was calculated on a single-sample basis if the reference robust multi-array average workflow was used for normalization. The prognostic prediction capability of 95 GC appears to be comparable to that of 21 GC . Moreover, their combination seems to result in the identification of more low-risk patients who do not need chemotherapy than either classification alone. The patients in the high-risk group were found to be more chemo-sensitive so that they can benefit more from adjuvant chemotherapy.