GRIPT: a novel case-control analysis method for Mendelian disease gene discovery

Table 1 Known disease genes were given high ranks and significant p values by GRIPT in a LCA cohort

Genes	No. of patients (%)	GRIPT		VAAST2		CMC		SKAT		KBAC
Genes	No. of patients (%)	Rank	p value	Rank	p value	Rank	p value	Rank	p value	Rank	p value
NMNAT1	4 (3.48%)	1	6.97E−39	7	2.50E−06	12	2.52E−09	18	1.78E−04	3	1.50E−05
GUCY2D	6 (5.21%)	2	3.40E−32	2	2.50E−06	102	1.15E−03	14	1.13E−04	35	1.84E−03
AIPL1	3 (2.61%)	3	2.03E−29	8	5.00E−06	100	1.08E−03	24	3.01E−04	40	2.15E−03
RPE65	3 (2.61%)	4	2.18E−29	4	2.50E−06	16	2.44E−08	4	0	2	7.00E−05
CEP290	7 (6.09%)	5	1.55E−26	1	2.50E−06	5	3.94E−11	2	0	1	2.00E−05
CRB1	3 (2.61%)	6	3.41E−22	12	2.44E−05	427	0.0231	77	2.14E−03	230	2.22E−02
RPGRIP1	4 (3.48%)	7	3.41E−22	3	2.50E−06	464	0.025	164	6.30E−03	168	1.50E−02
SPATA7	3 (2.61%)	8	4.55E−22	20	1.57E−04	1391	0.0838	534	3.16E−02	371	3.72E−02
TULP1	2 (1.74%)	9	6.53E−20	2689	0.158	15,160	0.7198	879	0.06	2203	0.2324
ADAM9	1 (0.87%)	12	7.33E−20	325	0.0198	790	0.0483	588	0.0357	243	0.0240
IFT140	4 (3.48%)	18	5.51E−13	499	0.0297	11,474	0.5064	3835	0.3333	7951	0.7111
TRNT1	1 (0.87%)	23	2.81E−10	7801	0.594	17,607	0.8925	8191	0.6	5775	0.5283

The listed genes are the correctly identified retinal disease genes among the top 20 candidate genes by GRIPT in the LCA cohort. Parameters: 115 cases, 5000 controls, the AR inheritance model

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