Table 1.
Single-variant and burden analyses of FANCM:p.Arg658*, p.Gln1701* and p.Arg1931* truncating variants in overall and country-restricted invasive breast cancer cases and controls
| Overall | ||||||
|---|---|---|---|---|---|---|
| Subgroup | Carriers | Non-carriers | Freq % | OR | 95% CI | P |
| FANCM:p.Arg658* | ||||||
| Controls | 19 | 53,717 | 0.035 | NA | ||
| All cases | 31 | 67,038 | 0.046 | 1.26 | 0.71–2.25 | 0.430 |
| ER-positive | 19 | 44,516 | 0.043 | 1.15 | 0.61–2.20 | 0.670 |
| ER-negative | 10 | 10,750 | 0.093 | 2.44 | 1.12–5.34 | 0.034 |
| TNBC | 7 | 4794 | 0.146 | 3.79 | 1.56–9.18 | 0.009 |
| FANCM:p.Gln1701* | ||||||
| Controls | 122 | 53,635 | 0.229 | NA | ||
| All cases | 155 | 66,951 | 0.232 | 1.09 | 0.85–1.38 | 0.798 |
| ER-positive | 97 | 44,467 | 0.218 | 1.02 | 0.78–1.34 | 0.893 |
| ER-negative | 21 | 10,748 | 0.204 | 0.97 | 0.61–1.56 | 0.369 |
| TNBC | 10 | 4794 | 0.229 | 1.09 | 0.57–2.10 | 0.149 |
| FANCM:p.Arg1931* | ||||||
| Controls | 96 | 53,633 | 0.179 | NA | ||
| All cases | 116 | 66,968 | 0.173 | 1.05 | 0.80–1.38 | 0.731 |
| ER-positive | 74 | 44,467 | 0.166 | 1.02 | 0.75–1.38 | 0.920 |
| ER-negative | 27 | 10,742 | 0.251 | 1.52 | 0.98–2.35 | 0.070 |
| TNBC | 10 | 4795 | 0.208 | 1.29 | 0.67–2.50 | 0.461 |
| All variantsa | ||||||
| Controls | 237 | 53,455 | 0.443 | NA | ||
| All cases | 302 | 66,736 | 0.452 | 1.02 | 0.86–1.21 | 0.823 |
| ER-positive | 190 | 44,323 | 0.427 | 0.96 | 0.79–1.16 | 0.698 |
| ER-negative | 58 | 10,700 | 0.548 | 1.23 | 0.92–1.64 | 0.154 |
| TNBC | 27 | 4773 | 0.583 | 1.32 | 0.89–1.95 | 0.167 |
| Country-restricted | ||||||
|---|---|---|---|---|---|---|
| Subgroup | Carriers | Non-carriers | Freq % | OR | 95% CI | P |
| FANCM:p.Arg658* | ||||||
| Controls | 19 | 48,887 | 0.039 | NA | ||
| All cases | 31 | 59,540 | 0.052 | 1.23 | 0.69–2.20 | 0.478 |
| ER-positive | 19 | 39,453 | 0.048 | 1.12 | 0.59–2.15 | 0.722 |
| ER-negative | 10 | 9613 | 0.104 | 2.31 | 1.05–5.07 | 0.047 |
| TNBC | 7 | 4283 | 0.163 | 3.56 | 1.46–8.69 | 0.011 |
| FANCM:p.Gln1701* | ||||||
| Controls | 120 | 48,506 | 0.249 | NA | ||
| All cases | 152 | 58,919 | 0.259 | 1.08 | 0.85–1.38 | 0.813 |
| ER-positive | 96 | 38,892 | 0.246 | 1.02 | 0.77–1.34 | 0.895 |
| ER-negative | 21 | 9558 | 0.230 | 0.97 | 0.60–1.56 | 0.368 |
| TNBC | 10 | 4197 | 0.261 | 1.09 | 0.56–2.10 | 0.150 |
| FANCM:p.Arg1931* | ||||||
| Controls | 77 | 34,988 | 0.220 | NA | ||
| All cases | 93 | 37,903 | 0.245 | 1.14 | 0.84–1.54 | 0.396 |
| ER-positive | 59 | 25,274 | 0.233 | 1.09 | 0.77–1.53 | 0.632 |
| ER-negative | 25 | 5920 | 0.421 | 1.96 | 1.24–3.10 | 0.006 |
| TNBC | 10 | 2614 | 0.381 | 1.77 | 0.91–3.45 | 0.116 |
| All variantsb | ||||||
| Controls | NA | |||||
| All cases | NA | |||||
| ER-positive | NA | |||||
| ER-negative | NA | |||||
| TNBC | NA | |||||
In bold are indicated the statistically significant results
Freq frequency, OR odds ratio CI confidence interval, P P-value, TNBC triple-negative breast cancer, NA not applicable
aThe burden analyses were performed by univariate logistic regression
bThese analyses were not possible in the country-restricted cases and controls as different countries were included for each variant. P-values were from Pearson chi-squared test