Table 1 Genes significantly associated with breast cancer risk using the MiXcan or PrediXcan approaches in 58,648 women, and the corresponding S-PrediXcan and GWAS results in a larger sample of 228,951 women of European ancestry

From: MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer

Gene Name

Cytoband

MiXcana

PrediXcanb

S-PrediXcanc

GWASd SNPs within 500 kb

  

Epithelial

Stromal

Combined

       
  

Effect

SE

P value

Effect

SE

P value

P value

Effect

SE

P value

Effect

SE

P value

 

Genes identified by both MiXcan and PrediXcan

CH17-437K3.1•

1p11.2

–1.62

0.28

7.3E–09

–1.62

0.28

7.3E–09

7.3E–09

–1.62

0.28

7.3E–09

–0.56

0.05

3.1E–28***

rs11249433

SLC4A7•

3p24.1

2.30

0.27

2.0E–17

2.30

0.27

2.0E–17

2.0E–17

2.30

0.27

2.0E–17

1.11

0.09

3.5E–38***

rs4973768

L3MBTL3•

6q23.1

–0.12

0.02

1.4E–08

–0.12

0.02

1.4E–08

1.4E–08

–0.12

0.02

1.4E–08

–0.11

0.02

2.1E–11***

rs6569648

RCCD1•

15q26.1

–0.16

0.03

4.2E–07

–0.16

0.03

4.2E–07

4.2E–07

–0.16

0.03

4.2E–07

–0.16

0.02

3.5E–11***

rs2290203

Genes identified by MiXcan only

MRPS30

5p12

3.00

0.67

6.8E–06

–4.82

0.75

1.8E–10

3.5E–10

–0.08

0.31

8.1E–01

0.50

0.04

3.3E–30***

rs10941679

SETD9

5q11.2

0.15

0.04

5.2E–04

–0.57

0.10

4.2E–09

8.4E–09

–0.07

0.02

1.8E–03

–0.10

0.02

1.9E–08***

rs62355902

ADGRV1

5q14.3

–0.27

0.05

3.6E–07

0.27

0.05

3.6E–07

3.6E–07

NA

NA

NA

–0.09

0.15

5.5E–01

rs10474352

ZNF703

8p11.23

–1.96

0.38

2.7E–07

1.59

0.27

2.4E–09

4.8E–09

0.07

0.08

3.9E–01

0.17

0.06

4.3E–03*

–

TMEM245

9q31.3

–0.64

0.12

7.0E–08

–0.30

0.10

2.2E–03

1.4E–07

–0.42

0.14

3.4E–03

0.04

0.07

5.4E–01

–

PRR33

11p15.5

–1.41

0.28

5.2E–07

1.41

0.28

5.2E–07

5.2E–07

NA

NA

NA

–1.39

0.14

1.4E–23***

rs3817198

CDYL2

16q23.2

–0.13

0.03

9.1E–07

–0.08

0.03

1.0E–03

1.8E–06

–2.67

0.85

1.7E–03

–0.10

0.04

3.7E–03*

rs13329835

PSG4

19q13.31

–0.16

0.04

3.0E–06

0.14

0.04

1.1E–04

5.9E–06

0.00

0.03

9.5E–01

0.01

0.01

5.3E–01

–

Genes identified by PrediXcan only

SRGAP2C

1p11.2

–0.19

0.25

4.3E–01

–0.58

0.28

4.1E–02

7.8E–02

–0.65

0.11

1.8E–09

–0.56

0.05

1.2E–28***

rs11249433

CASP8

2q33.1

–0.65

0.30

2.7E–02

0.43

0.27

1.1E–01

4.4E–02

–0.13

0.03

3.1E–06

–0.11

0.02

3.1E–11***

rs1830298

ALS2CR12

2q33.1

–0.10

0.12

4.0E–01

0.40

0.22

7.0E–02

1.3E–01

0.18

0.04

2.6E–06

0.15

0.02

4.2E–12***

rs1830298

STXBP4

17q22

–0.06

0.07

4.1E–01

0.18

0.05

2.1E–04

4.2E–04

0.16

0.03

4.5E–06

0.32

0.03

3.4E–23***

rs2787486

  1. aGenes with a MiXcan combined p value < 7.7 × 10−6 (0.05/6461 genes tested) aggregating across epithelial and stromal (non-epithelial) cell types were considered statistically significant. • denotes same model for epithelial and stromal cell types in MiXcan.
  2. bElastic net models were built using GTEx v8 mammary tissue data for 125 European ancestry women and all SNPs in the PredictDB database https://predictdb.org/. NA indicates that none of the SNPs evaluated were selected as predictors in the elastic net models for ADGRV1 and PRR33. Genes with a PrediXcan p value < 7.7 × 10−6 were considered statistically significant.
  3. cS-PrediXcan33 was used to test associations of predicted GReX with breast cancer risk using GWAS summary statistics for 122,977 cases and 105,974 controls11. *** denotes p value < 7.7 × 10−6 and * denotes p value < 0.05.
  4. dBreast cancer SNPs reported in a GWAS of 122,977 breast cancer cases and 105,974 controls11.
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