Table 3.
Biomarker pCR association results summary.
| Biomarker (sig) | Type | All HER2+ subtypes | HR+HER2+ subset | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TDM1/P (Exp: n = 52; RPPA: n = 49; IHC: n = 47) | THP (Exp: n = 44; RPPA: n = 43; IHC: n = 39) | Ctr (TH) (Exp: n = 31; RPPA: n = 25; IHC: n = 24) | TDM1/P (Exp: n = 35; RPPA: n = 34; IHC: n = 32) | THP (Exp: n = 29; RPPA:n = 29; IHC: n = 25) | |||||||||||||
| M1: pCR ~ sig | Adjust for HR M2: pCR ~ sig+HR | M1: pCR ~ sig | Adjust for HR M2: pCR ~ sig+HR | M1: pCR ~ sig | Adjust for HR M2: pCR ~ sig+HR | M1: pCR ~ sig | |||||||||||
| OR/unit increase | LR p | OR/unit increase | LR p | OR/unit increase | LR p | OR/unit increase | LR p | OR/unit increase | LR p | OR/unit increase | LR p | OR/unit increase | LR p | OR/unit increase | LR p | ||
| ER_PGR_avg | Continuous - mRNA | 0.413 [0.19–0.809] | 0.00893 | 0.228 [0.05–0.734] | 0.0109 | 0.243 [0.0921–0.531] | 0.000165 | 0.14 [0.0233–0.494] | 0.000939 | 0.487 [0.198–1.01] | 0.0538 | 0.542 [0.156–1.55] | 0.262 | 0.0985 [0.00976–0.473] | 0.00146 | 0.164 [0.0279–0.561] | 0.00214 |
| Mod7_ERBB2 | Continous - mRNA | 5.47 [2.43–15.6] | 4.84E-06 | 5.19 [2.36–14.5] | 5.71E-06 | 2.34 [1.24–4.88] | 0.00763 | 2.33 [1.2–4.96] | 0.0111 | 1.32 [0.593–3.1] | 0.5 | 1.13 [0.485–2.7] | 0.774 | 5.03 [1.99–16.9] | 0.000244 | 3.97 [1.61–13.2] | 0.00153 |
| Module11_Prolif_score | Continuous - mRNA | 2.18 [1.19–4.36] | 0.0111 | 2.1 [1.08–4.47] | 0.0293 | 2.55 [1.24–6.39] | 0.00861 | 2.4 [1.1–6.47] | 0.0254 | 1.77 [0.756–5.09] | 0.201 | 1.43 [0.556–4.29] | 0.471 | 3.28 [1.45–9.15] | 0.00311 | 1.63 [0.693–4.41] | 0.268 |
| ERBB2.total | Continuous - RPPA | 3.99 [1.96–9.51] | 4.56E-05 | 3.92 [1.92–9.31] | 6.02E-05 | 2.84 [1.46–6.18] | 0.00149 | 2.64 [1.33–5.88] | 0.00484 | 2.36 [0.794–8.81] | 0.125 | 1.98 [0.603–7.73] | 0.261 | 4.21 [1.77–12.8] | 0.000552 | 2.8 [1.23–7.58] | 0.0123 |
| ERBB2 Y1248 | Continuous - RPPA | 16.3 [2.56–245] | 0.000167 | 15.9 [2.64–217] | 0.00016 | 5.52 [1.45–31] | 0.00903 | 4.73 [1.23–25.4] | 0.0213 | 1.63 [0.597–4.61] | 0.32 | 1.08 [0.314–3.7] | 0.896 | 9.13 [1.78–113] | 0.00257 | 3.57 [0.837–20.7] | 0.0873 |
| EGFR Y1173 | Continuous - RPPA | 109 [5.96–5570] | 5.69E-06 | 123 [6.66–6230] | 3.67E-06 | 2.6 [1.01–10.6] | 0.0465 | 2.53 [0.949–9.73] | 0.0672 | 1.54 [0.492–4.6] | 0.43 | 0.979 [0.256–3.5] | 0.973 | 52.8 [3.49–2910] | 1.00E-04 | 2.12 [0.707–8.23] | 0.185 |
| Ki67 total | Continuous - RPPA | 1.24 [0.707–2.39] | 0.458 | 1.2 [0.677–2.31] | 0.535 | 1.83 [0.94–4.82] | 0.0798 | 1.56 [0.758–4.19] | 0.25 | 4.3 [0.809–32.5] | 0.0872 | 2.93 [0.437–26.9] | 0.271 | 7.15 [1.62–73.7] | 0.00286 | 0.961 [0.311–2.88] | 0.941 |
| Aurora A T288/B T232/C T198 | Continuous - RPPA | 1.3 [0.728–2.53] | 0.384 | 1.24 [0.683–2.46] | 0.485 | 4.75 [1.56–20.5] | 0.00364 | 4.22 [1.27–18.9] | 0.0171 | 1.06 [0.432–2.2] | 0.885 | 0.998 [0.31–2.16] | 0.996 | 4.01 [1.43–15.3] | 0.006 | 1.94 [0.421–10.3] | 0.396 |
| HER2 IHC (3+ vs. 2+/1+) | Categorical - IHC | 7.14 [1.4–50] | 0.0046 | 6.82 [1.6-36] | 0.0081 | 5.22 [0.86–40] | 0.031 | 3.98 [0.78–24] | 0.097 | n.a. | 0.046 | n.a. | 0.08 | 7.95 [1.17–96] | 0.0096 | 5.11 [0.64–68] | 0.060 |
| PAM50 subtype (HER2 vs others) | Categorical - mRNA | 20.6 [3.8–219] | 6.25E-06 | 41 [6.2–884] | 1.0E-05 | 1.55 [0.4–6.4] | 0.46 | 0.77 [0.16–3.3] | 0.73 | 4.5 [0.58–38] | 0.08 | 3.2 [0.45–24] | 0.24 | n.a. | 9.3E-04 | 1.09 [0.16–7.7] | 0.91 |
Bold indicates LR p < 0.05. *Because of the low number of patients with biomarker data who achieved pCR in the HR+HER2+ subset of the control arm (n < 4 pCR of 19 (Exp), 15 (RPPA), and 16 (IHC)), we do not calculate p-values.