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

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

Genes No. of patients (%) GRIPT VAAST2 CMC SKAT KBAC
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
  1. 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