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Table 2 HER2 co-amplification in breast cancer

From: HER2 is not a cancer subtype but rather a pan-cancer event and is highly enriched in AR-driven breast tumors

Chr

# Genes

Band

Start - end gene

Median amplified percentage in HER2A (IQR)

Median amplified percentage in non-HER2A (IQR)

3

1

3p25.1

MRPS25

4.2

1.1

3

5

3p24.1

KCNH8 - PP2D1

2.9 (0)

0.52 (0)

6

12

6q21

AIM1 - SNX3

7.5 (0.8)

2.6 (0.5)

10

10

10q22.3

ZMIZ1 - SFTPA1

6.5 (0.8)

1.7 (0.05)

11

34

11q12.3

NXF1 - PYGM

2.5 (0.4)

0.4 (0.06)

13

5

13q12.2-q12.3

FAM123A - SLC46A3

5.0 (0.4)

1.4 (0.3)

14

29

14q11.2

OR4K15 - RNASE1

4.2 (0.8)

0.7 (0.06)

14

15

14q11.2

OR5AU1 - OR4E2

3.4 (0.2)

0.6 (0.06)

17

55

17p11.2

LRRC48 - MTRNR2L1

5.0 (1.9)

1.5 (0.8)

17

419

17q11.1-q21.3

WSB1 - PPY

14.6 (12.3)

0.8 (0.7)

17

296

17q21.3-q24.3

NSF - MAP2K6

16.3 (7.3)

4.3 (1.7)

17

45

17q25.1

RPL38 - SAP30BP

9.2 (2.1)

2.9 (0.3)

20

3

20q13.2

ZFP64 - ZNF217

12.6 (0.8)

6.4 (0.6)

22

1

22q11.1

GAB4

2.5

0.3

  1. Genes that are significantly co-amplified with human epidermal growth factor receptor 2 (HER2) in The Cancer Genome Atlas (TCGA) and Metabric cohorts combined (Fisher’s exact false discovery rate (FDR) p value <0.05) (see Additional file 9E, Additional file 10). Median percentage of amplified genes (interquartile range, IQR) is shown per co-amplified region, in HER2 amplified (HER2A) and non-HER2A tumors