Table 2.
Detected haplotypes with frequency estimates for population controls and breast cancer cases
| RAD51 haplotype | Haplotype count | Frequency controls | Frequency all cases | Haplotype count | Frequency controls | Frequency fam cases |
| GCGCACTTAGAGAC | 1510 | 26.66% | 28.11% | 999 | 26.66% | 28.80% |
| GCGCATTTGGAGAC | 1510 | 27.22% | 27.63% | 996 | 27.22% | 27.36% |
| GCGTACTTAGGGAC | 956 | 18.07% | 16.81% | 656 | 18.07% | 17.74% |
| GTGCACTTAGAGAC | 913 | 16.25% | 16.89% | 579 | 16.25% | 15.03% |
| CCGCGCCGAAAGGG | 431 | 8.51% | 7.29% | 301 | 8.51% | 7.69% |
| GCTCATTTGGAGAC | 138 | 2.76% | 2.32% | 97 | 2.76% | 2.45% |
| GTGCACTTAGATAC | 37 | 0.45% | 0.86% | 21 | 0.45% | 0.84% |
| GCGCACTTAGGGAC | 2 | 0.04% | 0.03% | 2 | 0.04% | 0.08% |
| CCGCGCTTAGAGAC | 1 | 0.04% | 0% | 1 | 0.04% | 0% |
| GCGCACTTGGAGAC | 1 | 0.001% | 0.02% | 0 | 0% | 0% |
| CCGCGCCGAAAGAC | 1 | 0% | 0.03% | 0 | 0% | 0% |
| All BC cases vs controls: p = 0.45 | Familial BC cases vs controls: p = 0.66 | |||||
| XRCC3 haplotype | Haplotype count | Frequency controls | Frequency all cases | Haplotype count | Frequency controls | Frequency fam cases |
| CATGCGCGGG | 1599 | 28.57% | 29.58% | 1071 | 28.56% | 31.07% |
| TACGCGCTGG | 1586 | 28.32% | 29.25% | 1046 | 28.32% | 29.30% |
| CGTACGCGGG | 1159 | 22.33% | 20.05% | 778 | 22.33% | 19.17% |
| CATGCGCGGA | 602 | 10.82% | 10.98% | 378 | 10.83% | 9.26% |
| CGTGCGTGGG | 227 | 4.13% | 4.03% | 151 | 4.14% | 3.98% |
| TACGCGCTAG | 200 | 3.28% | 3.92% | 139 | 3.28% | 4.90% |
| CGTGCGCGGG | 75 | 1.49% | 1.25% | 55 | 1.49% | 1.52% |
| CGTACACGGG | 29 | 0.49% | 0.56% | 18 | 0.49% | 0.51% |
| CGTGTGCGGG | 17 | 0.41% | 0.23% | 12 | 0.41% | 0.17% |
| CGTGCGTGGA | 4 | 0.12% | 0.11% | 2 | 0.11% | 0.03% |
| TGCGCGCTGG | 1 | 0.05% | 0.005% | 1 | 0.05% | 0.003% |
| CATGCGCTGG | 1 | 0% | 0.02% | 1 | 0% | 0.04% |
| All BC cases vs controls: p = 0.49 | Familial BC cases vs controls: p = 0.14 | |||||
| XRCC2 haplotype | Haplotype count | Frequency controls | Frequency all cases | Haplotype count | Frequency controls | Frequency fam cases |
| GGGCGCACCT | 3633 | 66.79% | 65.48% | 2438 | 66.80% | 66.73% |
| GGGCGCACCG | 1253 | 22.53% | 22.97% | 814 | 22.53% | 21.79% |
| GGACGCACCT | 247 | 4.13% | 4.78% | 159 | 4.13% | 4.81% |
| GGGCCCATGT | 123 | 2.15% | 2.31% | 84 | 2.15% | 2.62% |
| AGGTGGACCT | 123 | 2.25% | 2.21% | 83 | 2.25% | 2.28% |
| GAGCGCGCGT | 119 | 2.11% | 2.21% | 73 | 2.11% | 1.77% |
| GGGCGCACGT | 1 | 0.02% | 0% | 1 | 0.02% | 0% |
| GAGCGCACCT | 1 | 0% | 0.02% | 0 | 0% | 0% |
| All BC cases vs controls: p = 0.55 | Familial BC cases vs controls: p = 0.80 | |||||
BC = breast cancer; Fam = familial.
Separate analyses were performed for all breast cancer cases versus controls and familial breast cancer cases versus controls. The SNPs included in the analysis are described in Table 3.