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Table 2 Association results of leading genes (top 10 genes, with P < 0.05 in 4 out of 12 methods)

From: Somatic mutations in benign breast disease tissues and association with breast cancer risk

Gene SKAT-O p SKAT-O p, weighted Logistic Regression OR Logistic Regression p Logistic Regression OR, weighted Logistic Regression p, weighted Analysis
MED12 0.0475* 0.0390* 0.9239 (0.8455, 0.9916) 0.0268* 0.8138 (0.66, 0.9681) 0.0189* Classic
0.0067** 0.0016** 0.9472 (0.8917, 0.9941) 0.0261* 0.8441 (0.7129, 0.9696) 0.0148* Liberal
0.0445* 0.0342* 0.9205 (0.8368, 0.9923) 0.0293* 0.8326 (0.686, 0.9721) 0.0189* Strict
MSH2 0.0203* 0.0445* 0.7539 (0.5546, 0.9418) 0.0078** 0.4294 (0.1775, 0.8518) 0.0085** Classic
0.0544 0.0856 0.8651 (0.7189, 0.9902) 0.0339* 0.618 (0.3305, 0.9584) 0.0277* Liberal
0.0284* 0.0145* 0.6938 (0.4566, 0.9331) 0.0097** 0.3202 (0.1025, 0.7632) 0.0043** Strict
BRIP1 0.0252* 0.1015 0.8686 (0.7356, 0.9874) 0.0301* 0.7081 (0.4852, 0.9707) 0.0313* Classic
0.0087** 0.0319* 0.8873 (0.7758, 0.9777) 0.0131* 0.7271 (0.5182, 0.9436) 0.0146* Liberal
0.0468* 0.0809 0.864 (0.7049, 1.002) 0.0542 0.7046 (0.4418, 0.9956) 0.0469* Strict
PMS1 0.0519 0.0935 0.8117 (0.6799, 0.949) 0.0081** 0.6126 (0.4005, 0.8929) 0.0101* Classic
0.0684 0.0842 0.8595 (0.745, 0.9704) 0.0134* 0.6628 (0.4569, 0.9149) 0.0116* Liberal
0.0165* 0.0136* 0.7846 (0.6447, 0.9309) 0.0047** 0.6053 (0.3996, 0.865) 0.0049** Strict
GATA3 0.0046** 0.2446 0.7949 (0.5809, 1.004) 0.0544 0.4899 (0.2246, 0.938) 0.0304* Classic
0.0130* 0.4957 0.8798 (0.7154, 1.043) 0.1439 0.6355 (0.3493, 1.059) 0.0832 Liberal
0.0051** 0.0175* 0.8086 (0.5848, 1.028) 0.0861 0.4766 (0.2047, 0.912) 0.0233* Strict
MUC16 0.0151* 0.0021** 0.9875 (0.9726, 0.999) 0.0327* 0.9588 (0.9153, 0.9927) 0.0157* Classic
0.1559 0.1089 0.9934 (0.9847, 1.001) 0.0746 0.9767 (0.9494, 0.9992) 0.0424* Liberal
0.1247 0.0875 0.988 (0.9723, 1) 0.0586 0.9664 (0.9259, 0.9982) 0.0376* Strict
EXT2 0.1100 0.1604 0.8305 (0.6589, 0.997) 0.0461* 0.5994 (0.3212, 1.01) 0.0549 Classic
0.0404* 0.0494* 0.8593 (0.72, 0.9822) 0.0244* 0.6348 (0.3789, 0.9543) 0.0277* Liberal
0.1435 0.1836 0.8292 (0.6447, 1.009) 0.0620 0.6434 (0.3599, 1.038) 0.0718 Strict
FAM175A 0.0657 0.1724 0.7249 (0.4568, 1.014) 0.0612 0.3819 (0.09252, 1.061) 0.0669 Classic
0.0103* 0.0181* 0.7172 (0.5108, 0.9316) 0.0095** 0.3513 (0.1179, 0.8153) 0.0114* Liberal
0.1628 0.1461 0.7465 (0.4696, 1.05) 0.0981 0.4276 (0.1126, 1.089) 0.0793 Strict
MLH1 0.1012 0.0885 0.8551 (0.7103, 1.005) 0.0573 0.6972 (0.4748, 0.9608) 0.0267* Classic
0.1320 0.0929 0.8819 (0.7573, 1.002) 0.0529 0.7201 (0.5073, 0.9604) 0.0244* Liberal
0.0895 0.0168* 0.8393 (0.672, 1.021) 0.0801 0.7335 (0.511, 0.9976) 0.0482* Strict
TGFB1 0.1689 0.1067 0.7878 (0.542, 1.077) 0.1381 0.5017 (0.1886, 1.029) 0.0610 Classic
0.0070** 0.0146* 0.7198 (0.5139, 0.9364) 0.0118* 0.4107 (0.1599, 0.8326) 0.0097** Liberal
0.6571 0.6260 0.8737 (0.5926, 1.236) 0.4487 0.6909 (0.2797, 1.412) 0.3246 Strict
  1. P values less than two thresholds: p < 0.05 (*), p < 0.01 (**)