Can multiple SNP testing in BRCA2 and BRCA1 female carriers be used to improve risk prediction models in conjunction with clinical assessment?

Prosperi, Mattia CF; Ingham, Sarah L; Howell, Anthony; Lalloo, Fiona; Buchan, Iain E; Evans, Dafydd Gareth

doi:10.1186/1472-6947-14-87

BMC Medical Informatics and Decision Making

Table 4 Multivariable cox regression fit on BRCA1 data set, overall and stratified by menopausal stage, with covariate set based on model (ii)

From: Can multiple SNP testing in BRCA2 and BRCA1 female carriers be used to improve risk prediction models in conjunction with clinical assessment?

Variable	BRCA1
	All subjects		Menopause		Ovulating
	AIC = 3175		AIC = 765		AIC = 591
	PH p-value > 0.0001		PH p-value = 0.0111		PH p-value = 0.5040
	RH (95% CI)	p-value	RH (95% CI)	p-value	RH (95% CI)	p-value
Year of birth	1.06 (1.05-1.08)	>0.0001	1.06 (1.03-1.09)	>0.0001	1.08 (1.04-1.11)	>0.0001
Manchester score	0.8 (0.61-1.05)	0.1013	0.35 (0.19-0.64)	0.0006	1.56 (0.83-2.91)	0.1635
GPS	0.76 (0.61-0.95)	0.0151	0.88 (0.54-1.45)	0.6248	0.58 (0.37-0.9)	0.0148
BMI	1.02 (0.98-1.06)	0.3942	1.01 (0.94-1.07)	0.844	1.13 (1.02-1.25)	0.0229
Parity q2 vs. q1	1.32 (0.91-1.89)	0.1389	1.99 (0.91-4.37)	0.0846	0.72 (0.32-1.63)	0.4298
Parity q3 vs. q1	1.21 (0.8-1.82)	0.377	1.24 (0.52-2.96)	0.6246	0.85 (0.36-2.04)	0.7228
Parity q4 vs. q1	1.61 (1.01-2.56)	0.046	1.88 (0.65-5.44)	0.2434	1.21 (0.43-3.4)	0.724
Parity missing vs. q1	1.22 (0.43-3.52)	0.7066	N/A	N/A	3.16 (0.34-28.9)	0.3089
Age of menarche q2 vs. q1	1.17 (0.82-1.67)	0.3914	1.14 (0.58-2.26)	0.6979	0.43 (0.17-1.07)	0.0695
Age of menarche q3 vs. q1	1.02 (0.67-1.54)	0.9345	1.02 (0.45-2.32)	0.9638	0.87 (0.45-1.71)	0.6918
Age of menarche q4 vs. q1	0.82 (0.55-1.23)	0.3437	1.34 (0.71-2.54)	0.3682	0.94 (0.4-2.16)	0.8772
Age of menarche missing vs. q1	1.12 (0.71-1.74)	0.6307	2.63 (0.86-8.03)	0.0902	1.49 (0.58-3.81)	0.4094
Age of menopause q2 vs. q1	0.37 (0.19-0.72)	0.0036	0.19 (0.09-0.43)	>0.0001
Age of menopause q3 vs. q1	0.39 (0.22-0.7)	0.0015	0.21 (0.1-0.45)	>0.0001
Age of menopause q4 vs. q1	0.33 (0.18-0.6)	0.0003	0.13 (0.06-0.28)	>0.0001
Age of menopause missing vs. q1	0.64 (0.39-1.04)	0.0708
Age of menopause not yet* vs. q1	4.48 (2.74-7.33)	>0.0001
Age of full-term pregnancy q2 vs. q1	1.22 (0.87-1.71)	0.2594	1.96 (0.98-3.91)	0.0576	1.06 (0.45-2.49)	0.8908
Age of full-term pregnancy q3 vs. q1	1.37 (0.96-1.96)	0.079	2.01 (0.94-4.32)	0.0734	2.06 (0.97-4.38)	0.0615
Age of full-term pregnancy q4 vs. q1	1.22 (0.81-1.84)	0.3512	2.8 (1.16-6.76)	0.0221	0.95 (0.34-2.64)	0.9163
Age of full-term pregnancy missing vs. q1	1.11 (0.7-1.79)	0.652	1.31 (0.45-3.8)	0.6245	0.98 (0.34-2.83)	0.9744
Age of full-term pregnancy not yet** vs. q1	2.17 (0.98-4.79)	0.0552	N/A	N/A	2.69 (0.77-9.34)	0.1198
Oral contraception usage q2 vs. q1	0.64 (0.39-1.04)	0.0704	0.4 (0.18-0.9)	0.0263	1.14 (0.39-3.33)	0.8105
Oral contraception usage q3 vs. q1	1.07 (0.71-1.62)	0.7575	0.48 (0.23-1)	0.0495	4.77 (1.77-12.83)	0.002
Oral contraception usage q4 vs. q1	1 (0.65-1.54)	0.9936	0.98 (0.46-2.07)	0.9571	2.13 (0.82-5.54)	0.1211
Oral contraception usage missing vs. q1	1.1 (0.72-1.66)	0.6686	0.4 (0.19-0.87)	0.0207	3.94 (1.42-10.94)	0.0084
Mastectomy	0.04 (0.01-0.31)	0.0018	0.05 (0.01-0.39)	0.0044	N/A	N/A
Oophorectomy	0.31 (0.16-0.58)	0.0003	0.3 (0.15-0.62)	0.0012	N/A	N/A

N/A: could not be fit in the model; q1 … q4: first to fourth age quartile, with the first being the youngest (~40 years old); *Ovulating; **Never had full term pregnancy.

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ISSN: 1472-6947

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