Table 1.
Three categories of variants associated with breast cancer risk in van Zitteren et al. l
| Gene | Variant in van Zitteren |
Variant in GWAS literature |
Allele Frequency in van Zitteren |
Per Allele Odds Ratio in van Zitteren |
Per Allele Odds Ratio in GWAS Literature |
P value in GWAS* |
Power to detect SNP in GWAS*† |
|---|---|---|---|---|---|---|---|
| Category 1: 18 SNPs found in GWAS | |||||||
| 1p11 | rs11249433 (T/C) | same | .3935 | 1.16 | 1.16 | 1×10-2 | |
| 2q35 | rs13387042 (G/A) | same | .500 | 1.11 | 1.12 | 2×10-10 | |
| 3p24 SLC4A7 | rs4973768 (C/T) | same | .470 | 1.12 | 1.11 | 6×10-7 | |
| 5p12 | rs2067980 (A/G) | rs10941679 | .160 | 1.08 | 1.19 | 3×10-3 | |
| 5p12 | rs7716600 (C/A) | .2205 | 1.10 | ||||
| 6q25 | rs2046210 (G/A) | same | .3645 | 1.36 | 1.15 | 2×10-5 | |
| 8q24 | rs13281615 (T/C) | same | .40 | 1.06 | 1.08 | 2×10-5 | |
| Chr 9 | rs1011970 (C/A) | Turnbull * | .1675 | 1.07 | 1.09 | 3×10-8 | |
| Chr 10 | rs2380205 (G/A) | Turnbull * | .4295 | 0.95 | 0.94 | 5×10-7 | |
| Chr 10 | rs10995190 (G/A) | Turnbull * | .149 | 0.84 | 0.86 | 5×10-15 | |
| Chr 10 | rs704010 (G/A) | Turnbull * | .3945 | 1.11 | 1.07 | 4×10-9 | |
| Chr 11 | rs614367 (G/A) | Turnbull * | .152 | 1.16 | 1.15 | 3×10-15 | |
| 14q24 | rs999737 (T/C) | .2385 | 0.94 | ||||
| 17q23 | rs6504950 (G/A) | .2700 | 1.04 | ||||
| FGFR2 | rs2981582 (C/T) | .379 | 1.18 | 1.26 | 4×10-31 | ||
| LSP1 | rs3817198 (T/C) | .300 | 1.06 | 1.07 | 6×10-4 | ||
| MAP3K1 | rs889312 (A/C) | .2795 | 1.13 | 1.12 | 5×10-9 | ||
| TNRC9 | rs3803662 (C/T) | .2505 | 1.23 | 1.19 | 3×10-15 | ||
|
| |||||||
| Category 2: 13 SNPs not found in GWAS | |||||||
|
| |||||||
| AKAP9 | M463I (G/T) | .366 | 1.08 | 0.087 | |||
| CCND1 | G870A | .4595 | 1.12 | 0.641 | |||
| CYP1B1 | Val432Leu (G/C) | .5445 | 1.60(het) | ||||
| 1.1(hom) | 1.00 | ||||||
| eNOS | G894T | .2265 | 1.22 (recess) | .010 | |||
| eNOS | T(−786)C | .8215 | 0.74 | 1.00 | |||
| ESR1 | rs3020314 (T/C) | .3105 | 1.05 | 0.002 | |||
| ESR2 | rs4986938 (A/G) | .361 | 0.94 | 0.017 | |||
| FAS | G(−1377)A | .148 | 1.18 | 0.710 | |||
| HER2 | I655V (G/A) | .1975 | 1.05 | 0.000 | |||
| IGFBP3 | A(−202)C | .4895 | 1.03 | 0.000 | |||
| NBS1 | G8360C | .320 | 0.97 | 0.000 | |||
| WDR79 | R68G C/G) | .1205 | 1.08 | 0.004 | |||
| XRCC1 | R399Q (A/G) | .660 | 1.12 (recess) | 0.078 | |||
|
| |||||||
| Category 3: 10 non-SNP variants | |||||||
|
| |||||||
| AR | CAG repeat | .539 | 0.61 (dom.) | ||||
| CASP8 | D302H | .444 | 0.89 | .88 | 0.14ns | ||
| CHEK2 | 1100delC | .500 binary | 2.40 | ||||
| Cyp19 | TTTA10 | 0.024 binary | 1.52 | ||||
| ERCC2 | A751C | .634 binary | 1.13 | ||||
| GSTM1 | Deletions | .565 binary | 1.10 | ||||
| GSTT1 | Deletions | .493 binary | 1.11 | ||||
| MTHFR | C677T | .336 binary | 1.04 | ||||
| TGFB1 | L10P | .5265 | 1.05 | ||||
| VDR | Fok1 | .146 binary | 1.14 | ||||
*
The GWAS was reported in (14).
†
Power calculations for category 2 SNPs (n=13) were performed at significance level 10−7 for the two-stage design of Turnbull et al (14). Power calculations for SNPs with recessive and co-dominant effects were based on a 2 degree of freedom test. For all other SNPs, the power calculations were done for the 1 degree of freedom trend test under a model that assumes that the relative odds are 1, OR, or OR2, for per allele odds ratio OR.