Table 1.
Prevalence and ORs for breast cancer risk of LoF variants in genes between selected Greek patients with breast cancer and reference controls from ExAC and FLOSSIES.
| Demokritos cases | Controls (ExAC/FLOSSIES) | Cancer risk (ExAC/FLOSSIES) | |||||||||||
| Gene | Truncating | Missense | Total | Cases (n) | Freq% | Truncating | Missense | Total | Controls (n) | Freq% | OR | 95% CI | P value |
| ATM | 13 | 3 | 16 | 1355 | 1.18 | 78/14 | 15/7 | 93/21 | 26862/7325 | 0.35/0.29 | 3.41/4.12 | 1.87 to 5.86/2 to 8.3 | 6.12×10−5/2.45×10−5 |
| CHEK2 | 7 | 12 | 19 | 1355 | 1.40 | 155/28 | 63/11 | 218/39 | 25819/7325 | 0.84/0.53 | 1.66/2.63 | 0.98 to 2.67/1.44 to 4.68 | 0.11/0.003 |
| CHEK2 miss | 0 | 12 | 12 | 1355 | 0.89 | 0/0 | 63/11 | 63/11 | 26974/7325 | 0.23/0.15 | 3.79/5.9 | 1.86 to 7.12/2.38 to 14.78 | 1.2×10−3/2.45× 10−4 |
| PALB2 | 7 | 0 | 7 | 1355 | 0.52 | 17/6 | 0/0 | 17/6 | 26435/7325 | 0.06/0.08 | 8.03/6.3 | 2.81 to 20.42/1.81 to 22.75 | 7.16×10−3/0.003 |
| RAD51C | 5 | 2 | 7 | 1355 | 0.52 | 19/2 | 3/1 | 22/3 | 26361/7325 | 0.08/0.04 | 6.19/12.6 | 2.23 to 15.03/2.87 to 75.64 | 0.002/4.73× 10−4 |
| TP53 | 2 | 6 | 7 | 1355 | 0.52 | 1/0 | 28/3 | 29/3 | 26889/7325 | 0.11/0.04 | 4.79/12.6 | 1.77 to 11.2/2.87 to 75.64 | 0.001/4.73× 10−4 |
CNV carriers, double LoF variant carriers and the low-risk CHEK2 variants: p.(Ile157Thr) and p.(Ser428Phe) were excluded from the analysis. Genes that had at least seven LoF variants were included. ExAC data extracted were non-TCGA/non-Finnish. FLOSSIES data extracted were on European-Americans.
Bold numbers indicate statistically significant findings.
ExAC, Exome Aggregation Consortium;FLOSSIES, Fabulous Ladies Over Seventy; Freq, variant observed frequency;LoF, loss-of-function; NA, not applicable; TCGA, The Cancer Genome Atlas; miss, missense.