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Table 2 Known disease genes were given high ranks and significant p values by GRIPT in a RP 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
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
  1. 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