Table 3 Biomarker pCR association results summary.

From: Neoadjuvant T-DM1/pertuzumab and paclitaxel/trastuzumab/pertuzumab for HER2+ breast cancer in the adaptively randomized I-SPY2 trial

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

  1. 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.
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