Clinical validation of a genetic model to estimate the risk of developing choroidal neovascular age-related macular degeneration

Hageman, Gregory S; Gehrs, Karen; Lejnine, Serguei; Bansal, Aruna T; DeAngelis, Margaret M; Guymer, Robyn H; Baird, Paul N; Allikmets, Rando; Deciu, Cosmin; Oeth, Paul; Perlee, Lorah T

doi:10.1186/1479-7364-5-5-420

Human Genomics

Table 15 Step 4. Effect rs12144939 is removed:

From: Clinical validation of a genetic model to estimate the risk of developing choroidal neovascular age-related macular degeneration

Model convergence status
Convergence criterion (GCONV = 1E-8) satisfied.
Model fit statistics
Criterion	Intercept only	Intercept and covariates
AIC	1317.356	1010.903
SC	1322.212	1059.457
-2 Log L	1315.356	990.903
Testing global null hypothesis: BETA = 0
Test	Chi-square	DF	Pr > ChiSq
Likelihood ratio	324.4536	9	<0.0001
Score	279.2738	9	<0.0001
Wald	209.2428	9	<0.0001
Residual Chi-square test
Chi-square	DF	Pr > ChiSq
2.6773	4	0.6132
Note: No (additional) effects met the 0.05 significance level for removal from the model.
Summary of backward elimination
Step	Effect removed	DF	Number in	Wald Chi-square	Pr > ChiSq
1	rs698859	1	12	0.0031	0.9559
2	rs1409153	1	11	0.3356	0.5624
3	rs1750311	1	10	0.3820	0.5366
4	rs12144939	1	9	1.9468	0.1629
Analysis of maximum likelihood estimates
Parameter	DF	Estimate	Standard error	Wald Chi-square	Pr > ChiSq
Intercept	1	-0.7554	0.2621	8.3051	0.0040
rs10490924	1	-1.4417	0.1245	134.0342	<0.0001
rs1061170	1	0.7697	0.2988	6.6352	0.0100
rs10922153	1	0.7240	0.1950	13.7839	0.0002
rs2230199	1	-0.4292	0.1286	11.1389	0.0008
rs2274700	1	0.8593	0.1695	25.7009	<0.0001
rs2990510	1	0.4556	0.1586	8.2557	0.0041
rs403846	1	-0.6775	0.3341	4.1118	0.0426
rs641153	1	0.8243	0.1999	17.0040	<0.0001
rs9332739	1	0.9509	0.3163	9.0360	0.0026
Odds ratio estimates
Effect	Point estimate	95% Wald confidence limits
rs10490924	0.237	0.185	0.302
rs1061170	2.159	1.202	3.878
rs10922153	2.063	1.407	3.023
rs2230199	0.651	0.506	0.838
rs2274700	2.362	1.694	3.292
rs2990510	1.577	1.156	2.152
rs403846	0.508	0.264	0.978
rs641153	2.280	1.541	3.374
rs9332739	2.588	1.392	4.811
Association of predicted probabilities and observed responses
Percentage concordant	81.5	Somers' D	0.637
Percentage discordant	17.9	Gamma	0.641
Percentage tied	0.6	Tau-a	0.319
Pairs	225094	c	0.818
Classification table
	Correct		Incorrect				Percentages
Prob. Level	Event	Non- event	Event	Non- event	Correct	Sensitivity	Specificity	False positive	False negative
0.000	467	0	482	0	49.2	100.0	0.0	50.8	--
0.020	467	3	479	0	49.5	100.0	0.6	50.6	0.0
0.040	467	20	462	0	51.3	100.0	4.1	49.7	0.0
0.060	467	35	447	0	52.9	100.0	7.3	48.9	0.0
0.080	467	49	433	0	54.4	100.0	10.2	48.1	0.0
0.100	465	65	417	2	55.8	99.6	13.5	47.3	3.0
0.120	461	91	391	6	58.2	98.7	18.9	45.9	6.2
0.140	457	113	369	10	60.1	97.9	23.4	44.7	8.1
0.160	450	143	339	17	62.5	96.4	29.7	43.0	10.6
0.180	448	159	323	19	64.0	95.9	33.0	41.9	10.7
0.200	442	182	300	25	65.8	94.6	37.8	40.4	12.1
0.220	438	200	282	29	67.2	93.8	41.5	39.2	12.7
0.240	435	213	269	32	68.3	93.1	44.2	38.2	13.1
0.260	434	217	265	33	68.6	92.9	45.0	37.9	13.2
0.280	423	227	255	44	68.5	90.6	47.1	37.6	16.2
0.300	422	246	236	45	70.4	90.4	51.0	35.9	15.5
0.320	419	252	230	48	70.7	89.7	52.3	35.4	16.0
0.340	414	271	211	53	72.2	88.7	56.2	33.8	16.4
0.360	410	274	208	57	72.1	87.8	56.8	33.7	17.2
0.380	389	287	195	78	71.2	83.3	59.5	33.4	21.4
0.400	385	303	179	82	72.5	82.4	62.9	31.7	21.3
0.420	381	312	170	86	73.0	81.6	64.7	30.9	21.6
0.440	365	326	156	102	72.8	78.2	67.6	29.9	23.8
0.460	361	331	151	106	72.9	77.3	68.7	29.5	24.3
0.480	358	340	142	109	73.6	76.7	70.5	28.4	24.3
0.500	344	354	128	123	73.6	73.7	73.4	27.1	25.8
0.520	332	357	125	135	72.6	71.1	74.1	27.4	27.4
0.540	324	366	116	143	72.7	69.4	75.9	26.4	28.1
0.560	315	378	104	152	73.0	67.5	78.4	24.8	28.7
0.580	300	389	93	167	72.6	64.2	80.7	23.7	30.0
0.600	293	392	90	174	72.2	62.7	81.3	23.5	30.7
0.620	284	398	84	183	71.9	60.8	82.6	22.8	31.5
0.640	266	410	72	201	71.2	57.0	85.1	21.3	32.9
0.660	252	417	65	215	70.5	54.0	86.5	20.5	34.0
0.680	236	423	59	231	69.4	50.5	87.8	20.0	35.3
0.700	233	427	55	234	69.5	49.9	88.6	19.1	35.4
0.720	196	440	42	271	67.0	42.0	91.3	17.6	38.1
0.740	190	441	41	277	66.5	40.7	91.5	17.7	38.6
0.760	179	448	34	288	66.1	38.3	92.9	16.0	39.1
0.780	170	453	29	297	65.6	36.4	94.0	14.6	39.6
0.800	127	456	26	340	61.4	27.2	94.6	17.0	42.7
0.820	114	467	15	353	61.2	24.4	96.9	11.6	43.0
0.840	103	467	15	364	60.1	22.1	96.9	12.7	43.8
0.860	77	470	12	390	57.6	16.5	97.5	13.5	45.3
0.880	65	471	11	402	56.5	13.9	97.7	14.5	46.0
0.900	53	475	7	414	55.6	11.3	98.5	11.7	46.6
0.920	40	479	3	427	54.7	8.6	99.4	7.0	47.1
0.940	16	481	1	451	52.4	3.4	99.8	5.9	48.4
0.960	9	481	1	458	51.6	1.9	99.8	10.0	48.8
0.980	1	481	1	466	50.8	0.2	99.8	50.0	49.2
1.000	0	482	0	467	50.8	0.0	100.0	--	49.2

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