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

Table 2 Known disease genes were given high ranks and significant p values by GRIPT in a RP 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
TULP1	3 (1.95%)	1	2.87E−22	15	1.57E−04	878	0.0429	279	0.0158	186	0.0190
EYS	8 (5.19%)	2	5.67E−18	2	2.50E−06	2718	0.1231	255	0.0143	504	0.0556
POMGNT1	2 (1.30%)	5	3.95E−15	854	0.0396	12,243	0.5391	8407	0.6	7477	0.6315
CNGA1	2 (1.30%)	6	3.95E−15	73	2.85E−03	18,620	0.9801	4650	0.375	4150	0.3769
RDH5	2 (1.30%)	7	3.95E−15	2430	0.119	2009	0.0924	1089	0.0769	900	0.0946
USH2A	13 (8.44%)	9	2.27E−14	1	2.50E−06	44	6.31E−05	6	0	6	0.0001
CRB1	3 (1.95%)	10	3.65E−11	114	4.66E−03	222	0.0063	428	0.028	92	0.0082
MERTK	3 (1.95%)	11	6.20E−11	19	0.0003	6523	0.2699	76	0.0023	1325	0.1384
BBS4	2 (1.30%)	13	8.51E−10	645	0.0297	13,022	0.5874	1309	0.0968	2036	0.1984
MAK	1 (0.649%)	17	6.25E−08	1694	0.0792	13,033	0.5874	11,162	0.75	3899	0.3573

The listed genes are the correctly identified retinal disease genes among the top 20 candidate genes by GRIPT in the RP cohort. Parameters: 154 cases, 5000 controls, the AR inheritance model

ISSN: 1474-760X