Table 3.
Associations of breast cancer with SNPs with MAF<0.05 among Asiansa
| Gene | SNP (alleles) annotationb | Chr:Positionc | Study | No. of cases/controlsd | EAF (no. of case/control)e | ORf | Lower 95% CI | Upper 95% CI | P valueg |
|---|---|---|---|---|---|---|---|---|---|
| BRCA1 | rs8176085 (T/C) | chr17:41274789 | BCAC | 26/1 | 0.0011 (26/1) | 26.98 | 12.65 | 57.55 | 3.33E−06 |
| Intron | |||||||||
| BRCA1 | rs799923 (A/G) | chr17:41251931 | BCAC | 92/77 | 0.0074 (95/85) | 1.82 | 1.34 | 2.47 | 9.65E−05 |
| Intron | |||||||||
| BRCA1 | rs8176173 (T/C) | chr17:41238619 | BCAC | 9/1 | 0.0004 (9/1) | 14.92 | 4.07 | 54.69 | 0.001 |
| Intron | |||||||||
| BRCA1 | rs8176258 (A/G) | chr17:41216021 | BCAC | 9/1 | 0.0004 (9/1) | 14.88 | 4.06 | 54.53 | 0.001 |
| Intron | |||||||||
| BRCA1 | rs8176305 (C/T) | chr17:41201364 | BCAC | 21/17 | 0.0015 (21/17) | 2.08 | 1.05 | 4.00 | 0.03 |
| Intron | |||||||||
| BRCA1 | rs273898669 (C/T) | chr17:41276135 | BCAC | 21/9 | 0.0012 (21/9) | 2.22 | 1.09 | 4.55 | 0.038 |
| Intron | |||||||||
| BRCA2 | rs80358978 (A/G) | chr13:32930651 | BCAC | 31/12 | 0.0017 (31/12) | 2.62 | 1.44 | 4.78 | 0.003 |
| Missense | SBCGS-Exomechip | 10/2 | 0.0009 (10/2) | 5.59 | 1.80 | 17.38 | 0.012 | ||
| Meta-analysis | 3.02 | 1.69 | 5.39 | 1.23E−04 | |||||
| BRCA2 | rs80359065 (T/G) | chr13:32937526 | BCAC | 162/128 | 0.0114 (164/128) | 1.43 | 1.13 | 1.80 | 0.003 |
| Missense | SBCGS-Exomechip | 93/82 | 0.0137 (93/83) | 1.24 | 0.92 | 1.67 | 0.157 | ||
| Meta-analysis | 1.35 | 1.13 | 1.63 | 0.001 | |||||
| BRCA2 | rs11571653 (G/A) | chr13:32910842 | BCAC | 221/323 | 0.023 (226/343) | 0.78 | 0.66 | 0.92 | 0.004 |
| Missense | SBCGS-Exomechip | 2/4 | 0.0005 (2/4) | 0.55 | 0.11 | 2.70 | 0.481 | ||
| Meta-analysis | 0.77 | 0.65 | 0.92 | 0.005 | |||||
| BRCA2 | rs28897700 (G/A) | chr13:32893344 | BCAC | 10/6 | 0.0006 (10/6) | 3.23 | 1.14 | 9.09 | 0.019 |
| Synonymous | |||||||||
| BRCA2 | rs11571789 (A/C) | chr13:32959240 | BCAC | 37/32 | 0.0027 (37/31) | 1.68 | 1.02 | 2.76 | 0.037 |
| Intron | |||||||||
| PTEN | rs1234218 (T/C) | chr10:89650759 | BCAC | 69/104 | 0.0068 (69/105) | 0.70 | 0.52 | 0.94 | 0.02 |
| Intron | |||||||||
| PTEN | rs3781195 (G/A) | chr10:89642609 | BCAC | 182/258 | 0.0177 (184/264) | 0.82 | 0.68 | 0.99 | 0.043 |
| Intron | |||||||||
| RAD51C | rs17175543 (G/T) | chr17:56803598 | BCAC | 45/50 | 0.9962 (6250/6618) | 0.65 | 0.43 | 1.00 | 0.042 |
| Intron |
aAll SNPs with meta-analysis P-value < 0.05 or P-value from BCAC < 0.05.
bEffect allele/reference allele based on forward strand.
cChromosome position (bp) based on NCBI Human Genome Build 37.
dNumber of samples carrying heterozygous variant.
eEffect allele frequency and number of cases and controls carrying effect allele are listed.
fOR (95% CI) was adjusted for study site (BCAC only), age, and PCs.
g P-value in each study obtained from logistic regression analysis. Meta-analysis p-value derived from a weighted z statistic-based meta-analysis.