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Table 2 Comparison of pre- and on-treatment biomarkers for predicting response and outcome. Evaluation of the performance of the top 10 pre- and on-treatment genes identified for predicting pathological response in the NEO dataset

From: On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer

  Response accuracy Response AUC Outcome (log-rank)
NEO I-SPY NEO I-SPY NEO I-SPY
On-treatment
 AAGAB 100% 78% 1.00 0.63 0.048 0.0036
 ZNF165 88% 54% 0.91 0.57 0.26 0.70
 KRTCAP3 79% 52% 0.85 0.56 0.81 0.49
 RFC2 79% 40% 0.85 0.35 0.51 0.44
 C20orf151 70% NA 0.75 NA 0.36 NA
 ARF5 70% 43% 0.75 0.36 0.0038 0.20
 BSPRY 70% 48% 0.75 0.49 0.47 0.19
 NGRN 58% NA 0.66 Na 0.53 Na
 CHST7 29% 46% 0.21 0.52 0.65 0.40
 SLC18B1 25% Na 0.18 NA 0.55 NA
Pre-treatment
 IGF1R 74% 63% 0.76 0.69 0.36 0.11
 CTNNB1 71% 49% 0.73 0.46 0.60 0.40
 SLC20A2 71% 56% 0.72 0.57 0.063 0.56
 HMGCL 68% 47% 0.67 0.45 0.10 0.97
 ST6GALNAC5 68% 52% 0.69 0.53 0.6 0.28
 AAGAB 65% 57% 0.65 0.58 0.71 0.20
 C1orf51 62% NA 0.61 NA 0.12 NA
 KRTCAP3 62% 54% 0.63 0.57 0.78 0.78
 SETDB2 50% 49% 0.48 0.51 0.29 0.15
 FADS2 29% 48% 0.27 0.5 0.14 0.73
  1. NA not available, gene not represented in I-SPY dataset; AUC area under curve. Bold indicates significant p-values. Italics indicate training prediction percentages