Although the overall molecular diagnostic rate for all probands was 52% (293/568), this diagnostic rate varied according to the types of hereditary eye diseases as follows (
Fig. 3A): 61% (124/202) for IRD, 49% (53/108) for retinal vessel disease, 53% (35/66) for eye tumors, 33% (19/58) for significant refractive error, 35% (16/46) for OPA, 46% (13/28) for RD, 48% (11/23) for ASD, and 59% for other rare hereditary eye diseases (those with fewer than 20 patients, including congenital motor nystagmus [53%, 9/17], congenital lens malformation [58%, 7/12], ocular albinism [67%, 4/6], and strabismus [100%, 2/2]). The rates of different diseases in the subgroup of inherited retinal degeneration were: 48% (32/66) for IRD, 63% (34/54) for RP, 57% (12/21) for MD, 73% (8/11) for STGD1, 74% (14/19) for LCA, 86% (12/14) for CORD, 75% (9/12) for RS, 100% (3/3) for BCD, and 50% (1/2) for CSNB. For most hereditary eye diseases, the diagnostic rates determined based on NGS-based OTSP were consistent with those found by WES or Sanger sequencing in our previous studies as well as those found in other reports (
Supplementary Table S3).
11,13,14,16,20,21,23–28,34,41–44 The only statistically significant difference (
P < 0.05) was observed for optic atrophy (
Supplementary Table S3); the molecular diagnostic rate for this disease was 35% according to NGS-based OTSP, whereas the rate was 10% according to Sanger sequencing in our previous study as well as in another study. The molecular diagnostic rate of NGS-based OSTP was similar between referrals from ophthalmologists from the section of Pediatric and Genetic Eye Diseases (56%, 146/259) and referrals from other sections (50%, 155/309). The most frequently mutated genes (those with diagnostic rates >1.5% in this population) were
RB1 (6%, 34/568),
FZD4 (3.5%, 20/568),
ABCA4 (3.5%, 20/568),
LRP5 (3.2%, 18/568),
RS1 (2.8%, 16/568),
TSPAN12 (2.5%, 14/568),
OPA1 (2.3%, 13/568),
CNGA3 (1.9%, 11/568), and
PAX6 (1.9%, 11/568;
Table 1). Three patients harbored PPVs in different genes, including
GRM6 c.1537G>A+
TSPAN12 c.1537G>A in #13427,
COL11A1 c.4177C>T+
LRP5 c.1996G>A in #11926, and
LRP5 c.4105_4106del+
FZD4 c.313A>G in #14731. Further clinical and genetic validation studies are needed to determine the pathogenetic reasons for the results observed in these patients. Of the 62 genes with mutations, 20 had mutations that were associated with different forms of diseases and affected 52.90% of the probands with identified mutations (155/293).