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Table 6 Associations with grade and lymph node status a

From: Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers

         

Affected by subtype, n (MAF)

 

Low-grade/no nodal involvement

High grade/nodal involvement

 

Subtype

Sample

SNP

Locus

Position b

Nearby gene

Ref c

Eff d

Reported e

High-grade/node-positive

Low-grade/node-negative

Unknown

Number unaffected (MAF)

HR (95% CI)

P -value

HR (95% CI)

P -value

P het-value f

Grade 3

BRCA1 carriers

rs17651413

2q33.1

202677054

KIAA2012

A

G

No

2,495 (0.12)

655 (0.11)

4,644 (0.13)

7,454 (0.11)

1.01 (0.86 to 1.2)

0.86

1.20 (1.12 to 1.29)

8.4 × 10−7

0.08

  

rs10069690

5p15.33

1332790

TERT

G

A

Yes

2,493 (0.3)

654 (0.29)

4,638 (0.3)

7,449 (0.26)

1.15 (1.02 to 1.29)

0.02

1.22 (1.16 to 1.29)

2.4 × 10−13

0.39

  

c6_pos151989450

6q25.1

151989450

C6orf97

G

A

Yes

2,497 (0.11)

655 (0.08)

4,645 (0.1)

7,455 (0.08)

1.01 (0.83 to 1.24)

0.91

1.31 (1.21 to 1.42)

2.2 × 10−11

0.02

  

rs8100241

19p13.11

17253894

ANKLE1

G

A

Yes

2,483 (0.48)

653 (0.52)

4,622 (0.48)

7,420 (0.52)

0.95 (0.86 to 1.05)

0.36

0.82 (0.78 to 0.86)

2.2 × 10−16

0.01

 

BRCA2 carriers

rs45631588

10q26

123341292

FGFR2

A

G

Yes

839 (0.44)

813 (0.48)

2,678 (0.44)

3,881 (0.39)

1.36 (1.24 to 1.49)

7.4 × 10−11

1.19 (1.09 to 1.3)

1.7 × 10−4

0.06

  

rs35850695

16q12.1

51131844

TOX3

G

A

Yes

839 (0.32)

813 (0.3)

2,678 (0.3)

3,881 (0.26)

1.2 (1.09 to 1.33)

3.0 × 10−4

1.31 (1.19 to 1.44)

4.0 × 10−8

0.26

Nodes

BRCA1 carriers

rs1498125

4q24

106412012

TET2

A

G

No

1,103 (0.2)

2,274 (0.23)

4,419 (0.22)

7,455 (0.2)

1.18 (1.1 to 1.25)

4.4 × 10−7

0.98 (0.89 to 1.09)

0.74

5.7 × 10−3

  

rs10069690

5p15.33

1332790

TERT

G

A

Yes

1,100 (0.3)

2,271 (0.29)

4,414 (0.3)

7,449 (0.26)

1.19 (1.12 to 1.26)

6.2 × 10−9

1.24 (1.13 to 1.35)

2.0 × 10−6

0.5

  

rs11743632

5q32

145389263

SH3RF2

G

A

No

1,103 (0.31)

2,274 (0.37)

4,418 (0.36)

7,453 (0.37)

1.05 (0.99 to 1.11)

0.1

0.8 (0.74 to 0.87)

2.3 × 10−7

6.9 × 10−7

  

rs9383936

6q25.1

151986307

C6orf97

G

A

Yes

1,103 (0.11)

2,274 (0.09)

4,420 (0.1)

7,455 (0.08)

1.16 (1.06 to 1.28)

1.3 × 10−3

1.41 (1.24 to 1.6)

1.3 × 10−7

0.03

  

rs2349485

7p22

8517481

NXPH1

A

C

No

1,091 (0.37)

2,249 (0.34)

4,374 (0.34)

7,398 (0.37)

0.87 (0.82 to 0.92)

8.5 × 10−7

0.97 (0.90 to 1.06)

0.53

0.03

  

rs11669059

19p13.11

17261453

ANKLE1

A

G

Yes

1,103 (0.41)

2,273 (0.4)

4,418 (0.39)

7,452 (0.43)

0.85 (0.81 to 0.9)

2.9 × 10−9

0.86 (0.80 to 0.93)

2.6 × 10−4

0.81

 

BRCA2 carriers

rs2981578

10q26

123330301

FGFR2

A

G

Yes

795 (0.44)

1,047 (0.48)

2,428 (0.47)

3,819 (0.52)

0.87 (0.8 to 0.94)

7.4 × 10−4

0.75 (0.68 to 0.82)

1.0 × 10−9

0.02

  

rs35850695

16q12.1

51131844

TOX3

G

A

Yes

804 (0.31)

1,068 (0.3)

2,458 (0.3)

3,881 (0.26)

1.22 (1.12 to 1.33)

8.5 × 10−6

1.30 (1.18 to 1.44)

2.6 × 10−7

0.36

  1. aCI, Confidence interval; HR, Hazard ratio; MAF, Mean allele frequency. Single-nucleotide polymorphisms (SNPs) associated at P <10−6 with high- or low-grade breast tumors and lymph node–positive or lymph node–negative breast cancer are shown. The most strongly associated SNPs from each locus are reported. bPosition in build 36. cReference allele. dEffect allele. eVariant located in previously reported breast cancer susceptibility locus. fP-value for the difference in association between high-grade breast cancer and low-grade breast cancer for grade 3 and for the association with lymph node–positive breast cancer and lymph node–negative breast cancer.
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Breast Cancer Research

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