Identification of 13 novel USH2A mutations in Chinese retinitis pigmentosa and Usher syndrome patients by targeted next-generation sequencing

Compound heterozygous mutations in GRM6 causing complete Schubert-Bornschein type congenital stationary night blindness

Background

To explore the genetic defects of a Chinese family with complete Schubert-Bornschein type congenital stationary night blindness (CSNB).

Methods

A Chinese family with complete Schubert-Bornschein type CSNB was enrolled in this study. The detailed ocular presentations of the patient were recorded. Targeted gene sequencing including 156 genes related to retinal diseases was used to detect the gene mutation. Sanger sequencing was performed to validate the potential pathogenic variants, and segregation analysis was performed on all available family members. Bioinformatics analysis was performed to predict the impact of the mutations.

Results

By targeted gene sequencing and Sanger sequencing, we identified compound heterozygous mutations in GRM6: c.152G>T (p.Gly51Val) and c.727delG (p.Val243SerfsX21). Segregation analysis demonstrated that the mother of the proband carried the missense mutation (c.152G>T) while her father carried the frameshift mutation (c.727delG), indicating CSNB was autosomal recessively inherited in this family. Several bioinformatics prediction programs revealed the mutations were "Damaging" or "Disease Causing" and conservation analysis showed both the codons Gly51 and Val243 were highly conserved among species, suggesting the changes were pathogenic.

Conclusion

By targeted gene sequencing and Sanger sequencing, we detected compound heterozygous mutations (c.152G>T, p.Gly51Val and c.727delG, p.Val243SerfsX21) in GRM6. The mutations co-segregated with the phenotype of the family members and are considered to be responsible for complete Schubert-Bornschein type CSNB. However, functional experiments in the future are needed to confirm the pathogenicity of the variants and to elucidate their exact molecular mechanisms causing CSNB.

Genetic Characteristics and Variation Spectrum of USH2A-Related Retinitis Pigmentosa and Usher Syndrome

Purposes: We aimed to characterize the USH2A genotypic spectrum in a Chinese cohort and provide a detailed genetic profile for Chinese patients with USH2A-IRD.

Methods: We designed a retrospective study wherein a total of 1,334 patients diagnosed with IRD were included as a study cohort, namely 1,278 RP and 56 USH patients, as well as other types of IEDs patients and healthy family members as a control cohort. The genotype-phenotype correlation of all participants with USH2A variant was evaluated.

Results: Etiological mutations in USH2A, the most common cause of RP and USH, were found in 16.34% (n = 218) genetically solved IRD patients, with prevalences of 14.87% (190/1,278) and 50% (28/56). After bioinformatics and QC processing, 768 distinct USH2A variants were detected in all participants, including 136 disease-causing mutations present in 665 alleles, distributed in 5.81% of all participants. Of these 136 mutations, 43 were novel, nine were founder mutations, and two hot spot mutations with allele count ≥10. Furthermore, 38.5% (84/218) of genetically solved USH2A-IRD patients were caused by at least one of both c.2802T>G and c.8559–2 A>G mutations, and 36.9% and 69.6% of the alleles in the RP and USH groups were truncating, respectively.

Conclusion: USH2A-related East Asian-specific founder and hot spot mutations were the major causes for Chinese RP and USH patients. Our study systematically delineated the genotype spectrum of USH2A-IRD, enabled accurate genetic diagnosis, and provided East Asian and other ethnicities with baseline data of a Chinese origin, which would better serve genetic counseling and therapeutic targets selection.

Review of Genotype-Phenotype Correlations in Usher Syndrome

Usher syndrome (USH) encompasses a group of clinically and genetically heterogenous disorders defined by the triad of sensorineural hearing loss (SNHL), vestibular dysfunction, and vision loss. USH is the most common cause of deaf blindness. USH is divided clinically into three subtypes-USH1, USH2, and USH3-based on symptom severity, progression, and age of onset. The underlying genetics of these USH forms are, however, significantly more complex, with over a dozen genes linked to the three primary clinical subtypes and other atypical USH phenotypes. Several of these genes are associated with other deaf-blindness syndromes that share significant clinical overlap with USH, pointing to the limits of a clinically based classification system. The genotype-phenotype relationships among USH forms also may vary significantly based on the location and type of mutation in the gene of interest. Understanding these genotype-phenotype relationships and associated natural disease histories is necessary for the successful development and application of gene-based therapies and precision medicine approaches to USH. Currently, the state of knowledge varies widely depending on the gene of interest. Recent studies utilizing next-generation sequencing technology have expanded the list of known pathogenic mutations in USH genes, identified new genes associated with USH-like phenotypes, and proposed algorithms to predict the phenotypic effects of specific categories of allelic variants. Further work is required to validate USH gene causality, and better define USH genotype-phenotype relationships and disease natural histories-particularly for rare mutations-to lay the groundwork for the future of USH treatment.

Targeted next-generation sequencing identifies ABCA4 mutations in Chinese families with childhood-onset and adult-onset Stargardt disease

Background: Stargardt disease (STGD) is the most common form of juvenile macular dystrophy associated with progressive central vision loss, and is agenetically and clinically heterogeneous disease. Molecular diagnosis is of great significance in aiding the clinical diagnosis, helping to determine the phenotypic severity and visual prognosis. In the present study, we determined the clinical and genetic features of seven childhood-onset and three adult-onset Chinese STGD families. We performed capture next-generation sequencing (NGS) of the probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes.

Methods: In all, ten unrelated Chinese families were enrolled. Panel-based NGS was performed to identify potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes, including the five known STGD genes (ABCA4, PROM1, PRPH2, VMD2, and ELOVL4). Variant analysis, Sanger validation, and segregation tests were utilized to validate the disease-causing mutations in these families.

Results: Using systematic data analysis with an established bioinformatics pipeline and segregation analysis, 17 pathogenic mutations in ABCA4 were identified in the 10 STGD families. Four of these mutations were novel: c.371delG, c.681T > G, c.5509C > T, and EX37del. Childhood-onset STGD was associated with severe visual loss, generalized retinal dysfunction and was due to more severe variants in ABCA4 than those found in adult-onset disease.

Conclusions: We expand the existing spectrum of STGD and reveal the genotype–phenotype relationships of the ABCA4 mutations in Chinese patients. Childhood-onset STGD lies at the severe end of the spectrum of ABCA4-associated retinal phenotypes.

USH2A gene variants cause Keratoconus and Usher syndrome phenotypes in Pakistani families

Background

Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy, affecting approximately 1 in 4000 individuals worldwide. The most common form of syndromic RP is Usher syndrome (USH) accounting for approximately 20–30 % of RP cases. Mutations in the USH2A gene cause a significant proportion of recessive non-syndromic RP and USH type II (USH2). This study aimed to determine the causative role of the USH2A gene in autosomal recessive inherited ocular diseases and to establish genotype-phenotype correlation associated with USH2A variants.

Methods

We performed direct Sanger sequencing and co-segregation analysis of the USH2A gene to identify disease causing variants in a non-syndromic RP family, two USH2 families and two Keratoconus (KC) families.

Results

Disease causing variants in the USH2A gene were identified in two families displayed KC and USH2 phenotypes. A novel variant c.4029T > G, p.Asn1343Lys in the USH2A gene was detected in a Pakistani family with KC phenotype. In addition, a missense variant (c.7334 C > T, p. Ser2445Phe) in the USH2A gene was found segregating in another Pakistani family with USH2 phenotype. Homozygosity of identified missense USH2A variants was found associated with autosomal recessive inherited KC and USH2 phenotypes in investigated families. These variants were not detected in ethnically matched healthy controls. Moreover, the USH2A variants were predicted to be deleterious or potentially disease causing by PolyPhen-2, PROVEAN and SIFT.

Conclusions

This study provided first evidence for association of a novel USH2A variant with KC phenotype in a Pakistani family as well as established the phenotype-genotype correlation of a USH2A variant (c.7334 C > T, p. Ser2445Phe) with USH2 phenotype in another Pakistani family. The phenotype-genotype correlations established in present study may improve clinical diagnosis of affected individuals for better management and counseling.

USH2A variants in Chinese patients with Usher syndrome type II and non-syndromic retinitis pigmentosa

Aims

To reveal the Usher syndrome type IIA (USH2A) gene variant profile in a large cohort of Chinese patients with non-syndromic retinitis pigmentosa (RP) or Usher syndrome type II (USH2) and to explore the genotype–phenotype correlation.

Methods

Targeted exome capture plus next-generation sequencing confirmed that 284 patients from 260 unrelated Chinese families carried USH2A disease-associated variants. Both personal medical history and family histories were reviewed. Ocular examinations were performed and audiograms were recorded if hearing loss was suspected. The genotype–phenotype correlation was evaluated by statistical analyses.

Results

A total of 230 variants in the USH2A gene were identified, of which 90 (39.13%) were novel. The most common variants in the RP and USH2 probands were p.Cys934Trp and p.Tyr2854_2894del, respectively, and 26.42% and 63.64% of the alleles in the RP and USH2 groups were truncating, respectively. Patients harbouring biallelic truncating variants had a younger age at the initial clinical visit and symptom onset than patients with missense variants; furthermore, the patients with USH2 had a younger age at the initial clinical visit and nyctalopia onset compared with the patients with RP (p<0.001). For the patients with USH2, the age of nyctalopia onset was positively correlated with that of hearing loss (p<0.05, r=0.219). In addition, three pseudo-dominant pedigrees were identified carrying biallelic USH2A variants.

Conclusions

This study enrolled the largest cohort of Chinese patients with USH2A and identified the most prevalent USH2A variants in USH2 and RP. We found that the patients with USH2 had more truncating variants and experienced an earlier decline in visual function. The findings enhance the current knowledge of USH2A heterogeneity and provide valuable information for future therapies.