Table 2. Associations between SNPs with the level of p-value<5.0×10-6 and disease-free survival (DFS) in breast cancer patients by tumor subtypes.
| SNP | Loci | Nearby gene | Alleles a | Discovery set | Replication set | Combined set | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MAF | HR b | (95% CI) | P | MAF c | HR b | (95% CI) | P | HR c | (95% CI) | P | |||||
| HR+ HER2- | |||||||||||||||
| rs161041 | 5q32 | PPP2R2B | C | T | 0.14 | 2.35 | (1.68–3.30) | 7.45×10-7 | 0.13 | 0.84 | (0.50–1.43) | 0.53 | 1.44 | (0.53–3.93) | 0.48 |
| rs2835688 | 21q22 | intergenic/DSCR3 | A | G | 0.26 | 2.65 | (1.71–4.11) | 1.40×10-6 | 0.27 | 1.07 | (0.73–1.56) | 0.74 | 1.67 | (0.68–4.07) | 0.26 |
| rs9935088 | 16q23 | WWOX | A | G | 0.41 | 2.00 | (1.50–2.66) | 1.98×10-6 | 0.41 | 0.91 | (0.64–1.29) | 0.58 | 1.35 | (0.62–2.94) | 0.44 |
| rs166870 d | 15q25 | intergenic/MTHFS | C | T | 0.13 | 2.34 | (1.64–3.35) | 3.16×10-6 | 0.87 | 2.13 | (1.07–4.23) | 0.03 | 2.30 | (1.67–3.15) | 2.88×10-7 |
| HR+ HER2+ | |||||||||||||||
| rs1896346 | 12q24 | intergenic/TBX3 | G | A | 0.38 | 0.12 | (0.05–0.28) | 1.09×10-6 | 0.44 | 1.08 | (0.62–1.88) | 0.80 | 0.37 | (0.04–3.13) | 0.36 |
| rs12940572 | 17q21 | LASP1 | T | C | 0.29 | 0.18 | (0.09–0.36) | 2.77×10-6 | 0.35 | 1.11 | (0.63–1.96) | 0.72 | 0.45 | (0.07–2.72) | 0.38 |
| HR- HER2+ | |||||||||||||||
| rs34073156 | 8q24 | intergenic/LOC100129367 | G | A | 0.10 | 4.14 | (2.26–7.60) | 4.58×10-6 | 0.07 | 1.27 | (0.48–3.35) | 0.64 | 2.44 | (0.77–7.74) | 0.13 |
| rs10906761 e | 10p13 | intergenic/CDNF | C | T | 0.49 | 0.26 | (0.14–0.47) | 4.94×10-6 | 0.48 | 0.95 | (0.54–1.68) | 0.87 | 0.50 | (0.14–1.80) | 0.29 |
| HR- HER2- | |||||||||||||||
| rs10825036 | 10q21 | intergenic/PCDH15 | T | G | 0.32 | 2.87 | (1.90–4.34) | 6.22×10-7 | 0.29 | 1.68 | (0.97–2.89) | 0.06 | 2.26 | (1.34–3.81) | 3.54×10-7 |
| rs10862597 | 12q21 | intergenic/RPL6P25 | C | G | 0.32 | 2.90 | (1.76–4.77) | 3.04×10-6 | 0.30 | 1.07 | (0.67–1.70) | 0.79 | 1.75 | (0.66–4.66) | 0.26 |
Abbreviations: SNP, single-nucleotide polymorphism; DFS, disease-free survival; RAF, risk-allele frequency; HR, hazard ratio; CI, confidence interval; MAF, minor allele frequency; HR, hormone receptor; HER2, human epidermal growth factor receptor 2.
aMajor and minor alleles.
bCox proportional hazard model adjusted for age, recruiting center, and TNM stage.
cRandom-effect meta-analysis of discovery and replication set.
dA proxy SNP, rs1081228, was genotyped for rs166870 in the replication set (r2 = 0.96 and D' = 1.00 in CHB+JPT).
eA proxy SNP,rs4750561, was genotyped for rs10906761 in the replication set (r2 = 1.00 and D' = 1.00 in CHB+JPT).