Table 4 Segregation analysis results allowing for parent-of-origin effects

From: Estimating single nucleotide polymorphism associations using pedigree data: applications to breast cancer

			Maternal		Paternal		Difference
SNP	Pedigrees	RAF (s.e.) ^a	HR (95% CI) ^b	P -value	HR (95% CI) ^b	P -value	δ (s.e.)	χ ²	P -value	logL	AIC
rs2981582	1626	0.401 (0.008)	1.26 (1.09–1.46)	0.002	1.13 (0.95–1.34)	0.157	−0.107 (0.150)	0.504	0.478	−5904.026	11814.05
rs1975930	1549	0.113 (0.005)	0.70 (0.55–0.90)	0.006	1.00 (0.83–1.20)	0.981	0.348 (0.194)	3.180	0.075	−2802.051	5610.10
rs10941679	1505	0.257 (0.010)	0.91 (0.62–1.32)	0.611	1.31 (0.94–1.81)	0.108	0.366 (0.347)	0.684	0.408	−1480.474	2966.95
rs3803662	1606	0.268 (0.007)	1.11 (0.99–1.25)	0.080	1.21 (1.07–1.38)	0.003	0.088 (0.109)	0.654	0.419	−5203.282	10412.56
rs2046210	1608	0.348 (0.007)	1.03 (0.91–1.16)	0.637	1.14 (1.00–1.30)	0.051	0.102 (0.112)	0.830	0.362	−5675.565	11357.13
rs614367	1627	0.152 (0.005)	1.23 (1.08–1.39)	0.001	0.98 (0.83–1.17)	0.863	−0.220 (0.134)	2.700	0.100	−3940.095	7886.19
rs10509168	1628	0.466 (0.008)	0.84 (0.75–0.95)	0.007	0.98 (0.86–1.12)	0.769	0.151 (0.118)	1.588	0.208	−5957.49	11920.98
rs1292011	1455	0.433 (0.011)	1.17 (0.92–1.49)	0.205	0.78 (0.59–1.03)	0.082	−0.400 (0.252)	1.628	0.202	−2176.575	4359.15
rs13387042	1598	0.489 (0.008)	1.16 (1.03–1.31)	0.014	1.20 (1.04–1.37)	0.010	0.030 (0.115)	0.068	0.795	−5904.889	11815.78
rs13281615	1608	0.401 (0.008)	1.09 (0.96–1.22)	0.178	1.10 (0.96–1.27)	0.155	0.017 (0.116)	0.022	0.882	−5585.132	11176.26
rs865686	1547	0.386 (0.008)	0.99 (0.87–1.14)	0.934	0.91 (0.77–1.06)	0.214	−0.093 (0.136)	0.468	0.494	−5397.179	10800.36
rs11249433	1609	0.414 (0.008)	1.06 (0.94–1.19)	0.346	1.05 (0.92–1.20)	0.486	−0.009 (0.114)	0.006	0.937	−5949.532	11905.06
rs2823093	1549	0.261 (0.007)	0.89 (0.77–1.02)	0.104	1.03 (0.89–1.20)	0.669	0.152 (0.133)	1.292	0.256	−4881.996	9769.99
rs3817198	1607	0.337 (0.007)	0.94 (0.84–1.06)	0.330	1.12 (0.99–1.27)	0.081	0.170 (0.108)	2.468	0.116	−5450.369	10906.74
rs889312	1605	0.283 (0.007)	1.01 (0.90–1.15)	0.811	1.14 (1.01–1.30)	0.042	0.119 (0.111)	1.152	0.283	−5180.945	10367.89
rs1011970	1628	0.172 (0.006)	1.05 (0.91–1.21)	0.489	0.99 (0.84–1.17)	0.912	−0.059 (0.136)	0.186	0.666	−4031.07	8068.14
rs17468277	1609	0.141 (0.005)	0.90 (0.72–1.14)	0.389	0.85 (0.65–1.10)	0.224	−0.062 (0.233)	0.072	0.788	−3351.337	6708.67
rs999737	1566	0.743 (0.007)	1.09 (0.95–1.25)	0.242	1.11 (0.94–1.30)	0.219	0.018 (0.136)	0.018	0.894	−4767.749	9541.50
rs2380205	1599	0.412 (0.010)	0.94 (0.76–1.16)	0.587	1.19 (0.95–1.49)	0.128	0.233 (0.210)	1.100	0.294	−2370.253	4746.51
rs4973768	1607	0.462 (0.008)	1.09 (0.96–1.23)	0.168	1.08 (0.94–1.24)	0.269	−0.009 (0.119)	0.006	0.937	−5904.616	11815.23
rs6504950	1609	0.288 (0.007)	1.02 (0.90–1.16)	0.724	0.94 (0.81–1.08)	0.379	−0.088 (0.122)	0.514	0.473	−5224.443	10454.89
rs2363956	1548	0.508 (0.008)	1.04 (0.92–1.19)	0.506	0.99 (0.86–1.14)	0.914	−0.051 (0.124)	0.170	0.680	−5362.528	10731.06
rs8170	1549	0.182 (0.006)	1.10 (0.95–1.27)	0.194	0.98 (0.82–1.17)	0.812	−0.116 (0.146)	0.620	0.431	−4062.888	8131.78
rs12662670	1549	0.076 (0.004)	1.26 (1.08–1.46)	0.004	1.08 (0.88–1.34)	0.460	−0.148 (0.161)	0.854	0.355	−2572.856	5151.71

Abbreviations: AIC=Akaike Information Criterion (Akaike, 1974); CI=confidence interval; χ²=1 df test statistic based on likelihood ratio test between the POE model and the standard major gene segregation model; δ=difference between maternal and paternal log HRs; HR=hazard ratio; logL=model maximum log-likelihood; RAF=risk allele frequency.
^aRAF is the maximum likelihood estimate of the risk allele frequency from the segregation analysis model.
^bPer-allele HR is reported such that the effect allele is the same as those from the population-based studies (Supplementary Table 1).

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Table 4 Segregation analysis results allowing for parent-of-origin effects

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