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

Winham, Stacey J.; Wang, Chen; Heinzen, Ethan P.; Bhagwate, Aditya; Liu, Yuanhang; McDonough, Samantha J.; Stallings-Mann, Melody L.; Frost, Marlene H.; Vierkant, Robert A.; Denison, Lori A.; Carter, Jodi M.; Sherman, Mark E.; Radisky, Derek C.; Degnim, Amy C.; Cunningham, Julie M.

doi:10.1186/s12920-021-01032-8

BMC Medical Genomics

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

P values less than two thresholds: p < 0.05 (*), p < 0.01 (**)

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