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Table 1 GWAS significant (P<5×10-8) and noteworthy (BFDP<0.15) results by subgroup, and corresponding results from adjusted analyses

From: Association of germline genetic variants with breast cancer-specific survival in patient subgroups defined by clinic-pathological variables related to tumor biology and type of systemic treatment

Subgroup

Variant

Chr

Position

Allelesa

AAF

Unadjusted analyses

Adjusted analyses

HR [95% CI]

P value

BFDP

HR [95% CI]

P value

BFDP

Grade 3 tumors

rs5934618b

X

9437463

A/G

0.08

1.39 [1.24,1.56]

1.7E-08

0.02

1.36 [1.21,1.53]e

3.0E-07

0.17

rs4830644b

X

9434808

A/G

0.08

1.39 [1.24,1.56]

2.0E-08

0.02

1.35 [1.20,1.52]e

4.8E-07

0.23

rs3810742b, c

X

9432603

T/C

0.08

1.38 [1.24,1.55]

2.0E-08

0.02

1.35 [1.20,1.52]e

4.2E-07

0.20

rs4830642b

X

9431786

T/C

0.08

1.38 [1.24,1.55]

2.9E-08

0.02

1.35 [1.20,1.52]e

5.8E-07

0.26

rs72611496b

X

9434264

G/A

0.08

1.38 [1.24,1.55]

4.3E-08

0.03

1.34 [1.19,1.51]e

1.2E-06

0.40

rs66871326

2

209048052

AAGGAG/A

0.76

0.85 [0.80,0.90]

2.1E-07

0.11

0.86 [0.81,0.92]e

1.8E-06

0.49

ER+ or PR+, and HER2-

rs8030394

15

71637241

C/T

0.99

2.47 [1.81,3.37]

1.1E-08

0.42

2.38 [1.74,3.27]f

7.6E-08

0.72

rs112641969

15

71715016

A/G

0.02

0.46 [0.35,0.61]

4.6E-08

0.46

0.48 [0.36,0.64]f

3.7E-07

0.78

rs16955466

15

71637757

C/T

0.01

0.40 [0.29,0.55]

1.5E-08

0.49

0.42 [0.31,0.58]f

1.8E-07

0.82

rs7165279

15

71636591

T/C

0.99

2.41 [1.77,3.28]

2.7E-08

0.54

2.33 [1.70,3.19]f

1.4E-07

0.78

rs111962948

15

71656213

G/T

0.01

0.41 [0.29,0.56]

3.0E-08

0.61

0.43 [0.31,0.60]f

5.6E-07

0.91

rs112813972

15

71577932

T/C

0.02

0.40 [0.28,0.55]

4.0E-08

0.70

0.42 [0.30,0.59]f

3.7E-07

0.90

ER+ or PR+, and HER2- treated with CT

rs62192052

2

230372348

C/T

0.02

0.15 [0.08, 0.28]

2.6E-09

0.99

0.15 [0.08, 0.29]g

5.5E-09

0.99

rs74423556c

2

230325234

C/G

0.02

0.16 [0.08,0.30]

2.1E-08

0.99

0.16 [0.08,0.31]g

3.8E-08

1.00

rs145983608

2

230296944

A/G

0.02

0.15 [0.08,0.30]

3.8E-08

1.00

0.15 [0.08,0.31]g

1.1E-07

1.00

ER+ or PR+, and HER2- not treated with CT

rs56248395b

11

20084391

C/T

0.13

2.33 [1.72,3.15]

4.8E-08

0.59

2.23 [1.66,2.99]g

1.2E-07

0.69

ER+ treated with ET

rs4679741

3

155003603

T/G

0.49

1.18 [1.11,1.26]

1.6E-07

0.09

1.20 [1.13,1.28] h

1.1E-08

0.01

ER- treated with CT

rs78754389d

4

35962454

G/A

0.07

1.79 [1.46,2.20]

1.7E-08

0.07

1.67 [1.39,2.00] i

4.1E-08

0.09

rs1106333

3

14562127

C/A

0.06

1.68 [1.39,2.03]

5.6E-08

0.12

1.70 [1.41,2.05] i

4.4E-08

0.11

rs117685664d

8

26989084

C/T

0.03

0.26 [0.16,0.42]

4.6E-08

0.97

0.50 [0.35,0.70]i

6.4E-05

0.99

Tamoxifen

rs72775397d

5

94266932

C/T

0.28

1.36 [1.21,1.53]

1.8E-07

0.11

1.11 [1.03,1.19]j

6.6E-03

1.00

Anthracylines

rs34072391

7

30243729

C/CA

0.52

1.27 [1.17,1.39]

6.2E-08

0.04

1.26 [1.15,1.37]k

3.4E-07

0.16

  1. Abbreviations: Chr chromosome, ER estrogen receptor, PR progesterone receptor, HER2 human epidermal growth factor receptor 2, ET Endocrine therapy, CT chemotherapy, AAF alternative allele frequency, HR hazard ratio, CI confidence interval, BFDP Bayesian False Discovery Probability
  2. Note: BFDP is computed assuming the prior probability of true association equal to 10-4for all variants, which implies a number of expected true associations in the order of 102. Results with BFDP<0.15 in the adjusted analyses are bolded. aReference/Alternative alleles, bAnalyses only include OncoArray data since the variants had imputation r2 <0.7 on iCOGS. More detailed analyses are reported in Table 2 and Supplementary Table 7, cVariant genotyped on OncoArray, dFrom the 5-years breast cancer specific survival analysis, eAdjusted for age at diagnosis, lymph node status, tumor size, distant metastases status, ER status, HER2 status, (neo)adjuvant CT, fAdjusted for age at diagnosis, lymph node status, tumor size, tumor grade, distant metastases status, and (neo)adjuvant CT, gAdjusted for age at diagnosis, lymph node status, tumor size, and tumor grade, hAdjusted for age at diagnosis, lymph node status, tumor size, tumor grade, HER2 status, (neo)adjuvant CT, iAdjusted for age at diagnosis, lymph node status, tumor size, tumor grade, and HER2 status, jAdjusted for age at diagnosis, lymph node status, tumor size, tumor grade, HER2 status ,and (neo)adjuvant CT, kAdjusted for age at diagnosis, lymph node status, tumor size, tumor grade, ER status, and HER2 status
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Breast Cancer Research

ISSN: 1465-542X

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