Table 1.
Novel candidate SNPs for familial AJ breast cancer.
| Pooled | Meta | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| SNP | Chr | MA | Dataset | MAFA | MAFU | Allelic p-value | OR | Genotypic p-value | Allelic P-value | OR | Genotypic P-value | Fisher Meta P | I2/Q |
| rs566164 | 6q21 | A | MSKCC | 0.32 | 0.24 | 4.37×10-3 | 1.49 | 1.55×10-2 | 6.67×10-6 | 1.45 | 6.31×10-5 | 2.00×10-4 | 0%/0.16 |
| BCFR | 0.36 | 0.29 | 1.50×10-2 | 1.41 | 5.36×10-2 | ||||||||
| NYUMC | 0.32 | 0.25 | 2.40×10-2 | 1.40 | 1.01×10-1 | ||||||||
|
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| rs16882214 | 6p22.3 | G* | MSKCC | 0.09 | 0.19 | 1.75×10-6 | 0.40 | 1.00×10-5 | 7.25×10-6 | 0.70 | 2.13×10-5 | 1.53×10-6 | 89%/18 |
| BCFR | 0.12 | 0.17 | 2.30×10-2 | 0.65 | 6.30×10-2 | ||||||||
| NYUMC | 0.15 | 0.12 | 1.96×10-1 | 1.28 | 3.50×10-2 | ||||||||
|
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| rs16956185 | 18p11.22 | A | MSKCC | 0.12 | 0.08 | 3.91×10-2 | 1.52 | 9.30×10-2 | 3.14×10-5 | 1.70 | 1.73×10-4 | 1.00×10-4 | 0%/1.2 |
| BCFR | 0.11 | 0.05 | 1.22×10-3 | 2.25 | 8.70×10-3 | ||||||||
| NYUMC | 0.13 | 0.08 | 2.66×10-2 | 1.62 | 1.21×10-2 | ||||||||
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| rs5965136 | Xq12 | A | MSKCC | 0.03 | 0.01 | 1.46×10-2 | 3.39 | 6.40×10-3 | 4.83×10-5 | 4.78 | 2.03×10-5 | 5.00×10-4 | 0%/1.0 |
| BCFR | 0.02 | 0.002 | 7.40×10-3 | 9.89 | 3.70×10-2 | ||||||||
| NYUMC | 0.012 | 0.002 | 4.91×10-2 | 6.53 | 1.19×10-1 | ||||||||
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| rs17663555 | 5q13.2 | G* | MSKCC | 0.61 | 0.48 | 2.09×10-3 | 1.66 | 9.85×10-3 | 5.74×10-5 | 1.38 | 3.82×10-4 | 5.00×10-4 | 0%/1.4 |
| BCFR | 0.58 | 0.52 | 1.53×10-2 | 1.26 | 5.82×10-3 | ||||||||
| NYUMC | 0.56 | 0.47 | 1.85×10-1 | 1.45 | 7.15×10-2 | ||||||||
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| rs12906542 | 15q24.3 | A | MSKCC | 0.04 | 0.07 | 3.65×10-2 | 0.54 | 3.22×10-2 | 6.70×10-6 | 0.50 | 7.12×10-6 | 7.34×10-7 | 80%/10 |
| BCFR | 0.007 | 0.07 | 9.90×10-7 | 0.09 | 2.20×10-7 | ||||||||
| NYUMC | 0.11 | 0.15 | 9.67×10-2 | 0.72 | 2.70×10-2 | ||||||||
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| rs11075884 | 16q22.2 | G | MSKCC | 0.22 | 0.28 | 2.43×10-2 | 0.72 | 2.49×10-2 | 9.15×10-3 | 0.80 | 1.31×10-4 | 7.00×10-4 | 80%/10 |
| BCFR | 0.20 | 0.29 | 1.24×10-3 | 0.61 | 3.78×10-3 | ||||||||
| NYUMC | 0.29 | 0.25 | 2.71×10-1 | 1.18 | 4.92×10-4 | ||||||||
*
G/C loci: minor allele = G on positive strand.
MA=minor allele; MAF=minor allele frequency for Cases (“A”) and Controls (“U”); p-values based on χ2 test on allele counts or genotype distribution between cases and controls. All 3 datasets were combined for pooled P-values and ORs and Fisher Meta-analysis. Cochran Q and I2 statistics for heterogeneity are reported (“I2/Q”).