Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing

Abstract

Background Leber congenital amaurosis (LCA) and juvenile retinitis pigmentosa (RP) are inherited retinal diseases that cause early onset severe visual impairment. An accurate molecular diagnosis can refine the clinical diagnosis and allow gene specific treatments. Methods We developed a capture panel that enriches the exonic DNA of 163 known retinal disease genes. Using this panel, we performed targeted next generation sequencing (NGS) for a large cohort of 179 unrelated and prescreened patients with the clinical diagnosis of LCA or juvenile RP. Systematic NGS data analysis, Sanger sequencing validation, and segregation analysis were utilised to identify the pathogenic mutations. Patients were revisited to examine the potential phenotypic ambiguity at the time of initial diagnosis. Results Pathogenic mutations for 72 patients (40%) were identified, including 45 novel mutations. Of these 72 patients, 58 carried mutations in known LCA or juvenile RP genes and exhibited corresponding phenotypes, while 14 carried mutations in retinal disease genes that were not consistent with their initial clinical diagnosis. We revisited patients in the latter case and found that homozygous mutations in PRPH2 can cause LCA/juvenile RP. Guided by the molecular diagnosis, we reclassified the clinical diagnosis in two patients. Conclusions We have identified a novel gene and a large number of novel mutations that are associated with LCA/juvenile RP. Our results highlight the importance of molecular diagnosis as an integral part of clinical diagnosis.

Mutations in MFSD8, Encoding a Lysosomal Membrane Protein, Are Associated with Nonsyndromic Autosomal Recessive Macular Dystrophy

“…51 More recently, several cases with retinitis pigmentosa, a single case of nonsyndromic Leber congenital amaurosis, and a single case of CRD have been described to carry mutations in CLN3. 52,53 Some of these mutations have been described to have a mild effect or result in a protracted phenotype. Most of these cases are far above the age threshold to develop neurologic NCL features, with the exception of 2 unrelated individuals (age 9 and 10 years) who are too young to exclude the development of nonocular features.…”

Genotype–phenotype correlation and mutation spectrum in a large cohort of patients with inherited retinal dystrophy revealed by next-generation sequencing

“…[3][4][5] Notably, this approach has been used for the development of next-generation molecular diagnosis of hereditary eye disorders. [6][7][8] Abu-Safieh and colleagues 6 designed an autozygome-guided screening panel in which they were able to successfully identify IRD in patients with six novel candidate genes. In another study, 163 known IRD genes were screened for by exome sequencing in 179 patients with Leber congenital amaurosis and juvenile RP, identifying a genetic predisposition in 40.2% (72/179) of the cases.…”

“…In another study, 163 known IRD genes were screened for by exome sequencing in 179 patients with Leber congenital amaurosis and juvenile RP, identifying a genetic predisposition in 40.2% (72/179) of the cases. 8 Further verifying this approach, Chen et al used targeted sequencing of 189 genes in members of 41 Chinese families with IRD and identified mutations occurring in 14 families. 9 In pilot studies, we successfully performed molecular diagnoses in patients with Usher syndrome and Bardet-Biedl syndrome by assessing a panel of 144 known genes.…”

Expanding the clinical, allelic, and locus heterogeneity of retinal dystrophies

“…This homozygous variant is absent in 615 Saudi exomes and in the ExAC browser (Supplementary Figure S2 online). ABCA4 [13] TULP1 [10] MERTK [8] CRB1 [7] RPE65 [7] RPGRIP1 [7] I MPG2 [6] KCNV2 [6] NR2E3 [6] RP1 [6] ALMS1 [5] CNGA3 [5] RDH12 [5] AIPL1 [4] CNGB1 [4] CRX [4] GUCY2D [4] SPATA7 [4] BBS2 [3] BBS4 [3] C8orf37 [3] CDHR1 [3] FAM161A [3] PDE6C [3] RLBP1 [3] USH2A [3] BBS10 [2] BBS5 [2] BBS7 [2] CERKL [2] CNNM4 [2] GRP179 [2] LRP5 [2] PDE6B [2] P ROM1 [2] PRPH2 [2] RP2 [2] SNRNP200 [2] ADAM9 [1] ADAMTS18 [1] ARL6 [1] BBS9 [1] BEST1 [1] C2ORF71 [1] CACNA1F [1] CEP290 [1] CHM [1] EFEMP1 [1] EYS …”

“…This technology is particularly suited for such a genetically and clinically heterogeneous condition as RD, and this has been demonstrated by several studies. [7][8][9][10][11][12][13] In this study, we describe the application of a next-generation sequencing-based gene panel strategy to study a very large cohort of RD patients in the diagnostic phase. In the discovery phase, we genotyped all familial cases that tested negative on the assay and identified three that mapped to a single locus and subjected them to whole-exome sequencing, which led us to identify AGBL5 and CDH16 as two novel RD candidate disease genes.…”