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 casesControls (ExAC/FLOSSIES)Cancer risk (ExAC/FLOSSIES)
GeneTruncatingMissenseTotalCases (n)Freq%TruncatingMissenseTotalControls (n)Freq%OR95% CIP value
ATM 1331613551.1878/1415/793/2126862/73250.35/0.293.41/4.121.87 to 5.86/2 to 8.36.12×10−5/2.45×10−5
CHEK2 7121913551.40155/2863/11218/3925819/73250.84/0.531.66/2.630.98 to 2.67/1.44 to 4.680.11/0.003
CHEK2 miss0121213550.890/063/1163/1126974/73250.23/0.153.79/5.91.86 to 7.12/2.38 to 14.78 1.2×10−3/2.45× 10−4
PALB2 70713550.5217/60/017/626435/73250.06/0.088.03/6.32.81 to 20.42/1.81 to 22.75 7.16×10−3/0.003
RAD51C 52713550.5219/23/122/326361/73250.08/0.046.19/12.62.23 to 15.03/2.87 to 75.64 0.002/4.73× 10−4
TP53 26713550.521/028/329/326889/73250.11/0.044.79/12.61.77 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.