Molecular Diagnosis of 34 Japanese Families with Leber Congenital Amaurosis Using Targeted Next Generation Sequencing

Abstract

Leber congenital amaurosis (LCA) is a genetically and clinically heterogeneous disease, and represents the most severe form of inherited retinal dystrophy (IRD). The present study reports the mutation spectra and frequency of known LCA and IRD-associated genes in 34 Japanese families with LCA (including three families that were previously reported). A total of 74 LCA- and IRD-associated genes were analysed via targeted-next generation sequencing (TS), while recently discovered LCA-associated genes, as well as known variants not able to be screened using this approach, were evaluated via additional Sanger sequencing, long-range polymerase chain reaction, and/or copy number variation analyses. The results of these analyses revealed 30 potential pathogenic variants in 12 (nine LCA-associated and three other IRD-associated) genes among 19 of the 34 analysed families. The most frequently mutated genes were CRB1, NMNAT1, and RPGRIP1. The results also showed the mutation spectra and frequencies identified in the analysed Japanese population to be distinctly different from those previously identified for other ethnic backgrounds. Finally, the present study, which is the first to conduct a NGS-based molecular diagnosis of a large Japanese LCA cohort, achieved a detection rate of approximately 56%, indicating that TS is a valuable method for molecular diagnosis of LCA cases in the Japanese population.

Clinical and Genetic Analysis of 63 Families Demonstrating Early and Advanced Characteristic Fundus as the Signature of CRB1 Mutations

“…11,12 Variants in CRB1 are one of the most common causes of autosomal recessive inherited retinal degeneration (IRD) and account for approximately 10% of patients with Leber congenital amaurosis (LCA) or early-onset retinal degeneration (EORD) from different populations. [13][14][15][16][17][18][19][20][21] A diversity of retinal degenerations has been reported to be associated with biallelic variants in CRB1, including the most severe LCA/EORD, 8,9 early-onset retinitis pigmentosa (RP), 1,10 and cone-rod dystrophy (CORD). 21 Highly variable clinical characteristics have been found in patients with biallelic variants in CRB1, such as Coat's like vasculopathy, 9,22 preserved para-arteriole retinal pigment epithelium (PPRPE), 10 pigmentations in various shapes 23 and macular involvement.…”

Single cell RNA sequencing reveals cellular diversity of trisomy 21 retina

“…Leber congenital amaurosis and Macular degeneration associated genes were enriched in RPCs(C0) with the P value less than 0.05. Also, we noticed that C0 specifically expressed RPE65, OTX2, LRAT and BEST1 34,35 . While Optic atrophy associated genes was enriched in astrocyte(C2), where NR2F1 36 and AFG3L2 37 were highly expressed.…”

Long‐term observation of a Japanese mucolipidosis IV patient with a novel homozygous p.F313del variant of MCOLN1

“…We dealt with common genetic variants (allele frequency >0.01 for recessive variants or >0.001 for dominant variants) in the following databases and in‐house exome data ( n = 218) as putative non‐pathogenic sequence alterations: 1000 Genomes Project database (https://www.internationalgenome.org/), Genome Aggregation Database (https://gnomad.broadinstitute.org/), Tohoku Medical Megabank database (https://ijgvd.megabank.tohoku.ac.jp/) and Human Genetic Variation Database (http://www.genome.med.kyoto-u.ac.jp/SnpDB/). Identified variants were filtered by applying our prioritization criteria as previously described (Hosono et al, 2018).…”