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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