Table 2 Differences in characteristics between two types of breast cancer classified by hormone receptor status

Response to neoadjuvant chemotherapy

 pCR (grade 3)

8 (8)

12 (11)

0.009 (0.034)

 No pCR (grade 0–2)

14 (9)

3 (2)

HER2 copy numbers

 ≤ 2.0

6

2

0.368

 > 2.0

22

16

Wild-type HER2 mRNA

 < 400

16 (13)

7 (5)

0.05 (0.044)

 ≥ 400

7 (7)

11 (11)

ΔHER2 mRNA

 < 4.5

16 (13)

3 (2)

<0.001 (0.001)

 ≥ 4.5

7 (7)

15 (14)

Percentages of ΔHER2 mRNA

 < 2.4%

20 (18)

15 (14)

0.745 (0.813)

 ≥ 2.4%

3 (2)

3 (2)

PI3KCA (exons 9 and 20)

 Wild-type

24 (19)

16 (14)

0.755 (0.418)

 Mutated

4 (1)

2 (2)

PI3KCA (exons 9 and 20)

 Wild-type + Normal + Loss + UPD

19 (18)

12 (12)

0.933 (0.611)

 Mutated + Gain

9 (4)

6 (4)

PTEN

 Normal + Gain + UPD

23 (20)

18 (16)

0.058 (0.215)

 Loss

5 (2)

0 (0)

INPP4B

 Normal + Gain + UPD

24 (20)

16 (14)

0.755 (0.735)

 Loss

4 (2)

2 (2)

PI3KCA , PTEN, INPP4B

 No aberrations*

15 (15)

10 (9)

0.895 (0.452)

 Aberrations**

13 (7)

8 (7)

DEK

 Normal

19 (17)

11 (11)

0.639 (0.556)

 Gain

9 (5)

7 (5)

FGFR1

 Normal + Loss + UPD

18 (15)

13 (12)

0.575 (0.871)

 Gain

10 (7)

5 (4)

CCND1

 Normal + Loss

16 (13)

9 (8)

0.635 (0.578)

 Gain

12 (9)

9 (8)

FOXA1

 Normal + UPD

20 (18)

13 (11)

0.953 (0.35)

 Gain

8 (4)

5 (5)

CDH3

 Normal + Loss + UPD

23 (19)

18 (16)

0.058 (0.124)

 Gain

5 (3)

0 (0)

BIRC5

 Normal + Loss + UPD

22 (17)

8 (6)

0.018 (0.013)

 Gain

6 (5)

10 (10)

MYBL2

 Normal + Loss

18 (15)

14 (13)

0.332 (0.366)

 Gain

10 (7)

4 (3)

AIB1

 Normal + Loss

19 (15)

14 (13)

0.466 (0.366)

 Gain

9 (7)

4 (3)