Modeling of multivariate longitudinal phenotypes in family genetic studies with Bayesian multiplicity adjustment

Ding, Lili; Kurowski, Brad G; He, Hua; Alexander, Eileen S; Mersha, Tesfaye B; Fardo, David W; Zhang, Xue; Pilipenko, Valentina V; Kottyan, Leah; Martin, Lisa J

doi:10.1186/1753-6561-8-S1-S69

BMC Proceedings

Table 1 Posterior inclusion probabilities of the causal SNVs

From: Modeling of multivariate longitudinal phenotypes in family genetic studies with Bayesian multiplicity adjustment

					Number of noise variables
Causal SNV	Position	MAF			1		15		30		60		90		90* (UNI)		90* (MGA)
			D	S	D	S	D	S	D	S	D	S	D	S	D	S	D	S
1	47912898	0.0049	1.71	2.34	0.06	0.11	0.03	0.06	0.02	0.05	0.01	0.02	0.01	0.01	0.03	0.04	2.0E-01	1.7E-01
2	47913455	0.0049	−5.46	−8.70	*0.93*	*0.75*	*0.93*	*0.84*	*0.87*	*0.76*	*0.51*	0.22	0.33	0.09	0.99	0.41	6.3E-03	1.4E-02
3	47924216	0.0066	1.35	1.84	0.03	0.04	0.02	0.02	0.01	0.01	0.01	0.01	0.00	0.00	0.01	0.01	2.3E-01	4.6E-01
4	47955326	0.0066	−1.93	−2.63	0.05	0.08	0.02	0.03	0.01	0.03	0.01	0.01	0.00	0.01	0.01	0.02	5.8E-01	4.6E-01
5	47956424^a	0.3777	−1.50	−2.38	*0.52*	0.32	0.06	0.02	0.09	0.03	0.08	0.06	0.03	0.01	0.09	0.07	4.2E-07	1.2E-04
6	47957741	0.0016	−5.08	−8.10	0.06	0.08	0.03	0.05	0.02	0.04	0.01	0.01	0.01	0.01	0.01	0.01	9.7E-01	4.4E-01
7	47957996^b	0.0301	−4.64	−7.39	0.11	*0.64*	0.09	*0.65*	0.06	*0.71*	0.06	*0.56*	0.10	*0.51*	0.08	0.31	9.7E-12	4.0E-14
8	47958037^a	0.3420	0.00	−0.00	0.22	0.33	0.06	0.06	0.05	0.06	0.02	0.05	0.02	0.02	0.05	0.08	3.3E-07	4.3E-05
9	47973345	0.0082	2.14	2.92	0.08	*0.58*	0.04	0.47	0.03	0.42	0.02	0.19	0.01	0.12	0.01	0.09	1.9E-05	6.6E-03
10	48040283^b	0.0318	−6.22	−9.91	*0.97*	*0.52*	*0.95*	0.45	*0.96*	0.36	*0.96*	0.46	*0.91*	*0.51*	0.94	0.71	2.6E-13	2.3E-14
11	48040284	0.0131	−6.95	−11.1	0.42	0.38	0.12	0.08	0.08	0.07	0.05	0.04	0.03	0.02	0.35	0.26	5.9E-03	2.4E-03
12	48054461	0.1187	0.46	0.63	0.10	0.05	0.14	0.08	0.07	0.04	0.01	0.00	0.01	0.00	0.13	0.02	1.4E-02	3.0E-02
13	48061725	0.0050	1.79	2.44	0.08	0.07	0.04	0.03	0.03	0.03	0.01	0.01	0.01	0.01	0.02	0.01	9.4E-01	7.4E-01
14	48069438	0.0065	−1.78	−2.43	0.04	0.11	0.02	0.04	0.01	0.03	0.01	0.02	0.00	0.01	0.01	0.03	4.2E-01	6.7E-01
15	48091219	0.0065	2.54	3.46	0.06	0.09	0.03	0.04	0.02	0.03	0.01	0.01	0.01	0.01	0.01	0.02	7.2E-01	5.6E-01
True positives					3	4	2	2	2	2	2	1	1	2	2	1	5	4
False positives					0	0	0	0	0	0	0	0	0	0	1	1	8	6

Numbers in italics show the results of the Bayesian bivariate model, that is, estimated posterior inclusion probabilities of the 15 causal SNVs and numbers of true and false positives based on the median probability model. Posterior inclusion probabilities ≥0.5 are in bold. The last 4 columns are the results of the model where DBP and SBP are modeled independently (*) using either the Bayesian univariate model (UNI, posterior inclusion probability) or measured genotype approach (MGA, p value), where p values in bold are below the cutoff with Bonferroni correction (0.05/105 = 4.76E-04). In the table, D represents DBP, S represents SBP. SNVs 5 and 8 (^a) and SNVs 7 and 10 (^b) have relatively high LD (r²≥0.8).

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ISSN: 1753-6561

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