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Table 3 Nominally significant rare-variant tests for breast cancer overall and by estrogen receptor status, across all ethnicities

From: Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities

Outcome

Gene

Chromosome: index SNP

Number of variants

CP

Significant test(s)

p value

OR (95 % CI)

Breast cancer overall

ORAOV1

Chr11: rs614367

43

4.80 %

SKAT

0.004

0.8 (0.6–1.1)

 

GTPBP3

Chr19: rs8170

48

3.50 %

SKAT

0.01

1.3 (0.9–1.8)

 

GLT25D1

Chr19: rs8170

55

2.50 %

SKAT

0.015

0.9 (0.7–1.4)

 

DDA1 - p2

Chr19: rs8170

1

<1.0 %

SKAT

0.046

2.0 (0.9–4.1)

 

NSMCE4A

Chr10: rs2981579

17

0.70 %

BURDEN

0.023

0.4 (0.2–0.9)

 

ANO8 - p2

Chr19: rs8170

8

<1.7 %

BURDEN

0.034

5.3 (1.1–24.2)

ER+

GTPBP3

Chr19: rs8170

48

3.50 %

SKAT

0.007

1.4 (1.0–2.1)

 

TMEM221 - p2

Chr19: rs8170

5

<2.1 %

SKAT

0.013

0.4 (0.2–1.0)

 

GLT25D1

Chr19: rs8170

55

2.50 %

SKAT

0.018

0.8 (0.5–1.3)

 

ZNF365 - p2

Chr10: rs10995190

8

<2.0 %

SKAT, BURDEN

0.019

2.5 (1.0–5.9)

 

ORAOV1

Chr11: rs614367

43

4.80 %

SKAT

0.024

0.8 (0.6–1.1)

 

TMEM221

Chr19: rs8170

24

2.10 %

SKAT

0.028

0.6 (0.4–1.1)

 

ZFYVE26

Chr14: rs999737

126

5.70 %

SKAT

0.041

1.2 (0.9–1.5)

 

MAP1S - p2

Chr19: rs8170

22

<4.9 %

SKAT

0.045

0.9 (0.6–1.5)

 

GLT25D1 - p2

Chr19: rs8170

15

<2.5 %

SKAT

0.049

0.9 (0.4–1.9)

 

ZNF365

Chr10: rs10995190

38

2.00 %

BURDEN

0.013

1.8 (1.1–2.9)

 

PLVAP

Chr19: rs8170

31

1.80 %

BURDEN

0.016

1.8 (1.1–3.0)

 

FGFR2

Chr10: rs2981579

41

1.50 %

BURDEN

0.016

2.0 (1.1–3.4)

 

C6orf211

Chr6: rs2046210

34

2.70 %

BURDEN

0.044

0.6 (0.4–1.0)

ER−

ORAOV1

Chr11: rs614367

43

4.80 %

SKAT

0.028

0.9 (0.5–1.4)

 

ANO8 - p2

Chr19: rs8170

8

<1.7 %

SKAT

0.028

4.4 (0.3–74.5)

 

FAM129C

Chr19: rs8170

62

6.80 %

SKAT

0.035

0.9 (0.6–1.3)

 

BABAM1

Chr19: rs8170

24

1.40 %

SKAT

0.041

2.1 (0.9–5.1)

 

ORAOV1 - p2

Chr11: rs614367

2

<4.8 %

SKAT

0.042

3.3E + 06 (0.0– > 1E50)

 

UNC13A

Chr19: rs8170

69

3.70 %

SKAT

0.045

1.5 (0.9–2.5)

 

ZFYVE26

Chr14: rs999737

126

5.70 %

SKAT

0.049

1.5 (1.0–2.3)

 

USE1

Chr19: rs8170

14

0.40 %

BURDEN, SKAT

0.022

7.2 (1.3–38.8)

 

ABHD8

Chr19: rs8170

19

1.30 %

BURDEN

0.026

2.4 (1.1–5.0)

 

TMEM221

Chr19: rs8170

24

2.10 %

BURDEN

0.029

2.1 (1.1–3.9)

 

ZFYVE26 - p2

Chr14: rs999737

29

<5.7 %

BURDEN

0.031

2.5 (1.1–5.7)

  1. Abbreviations: SNP Single-nucleotide polymorphism, p2 Subset of variants within gene predicted to be potentially or possibly damaging by Polymorphism Phenotyping version 2, CP Carrier proportion or proportion of subjects who carry at least one rare, nonsynonymous variant in gene, BURDEN Inverse-variance-weighted burden test, SKAT Meta-analysis of sequence kernel association test assuming the effect of each variant is homogeneous, regardless of ethnicity
  2. Underlining = lowest p value if more than one significant test
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Breast Cancer Research

ISSN: 1465-542X

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