Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families

Abstract

Usher syndrome (USH) is a leading cause of deaf-blindness in autosomal recessive trait. Phenotypic and genetic heterogeneities in USH make molecular diagnosis much difficult. This is a pilot study aiming to develop an approach based on next-generation sequencing to determine the genetic defects in patients with USH or allied diseases precisely and effectively. Eight affected patients and twelve unaffected relatives from five unrelated Chinese USH families, including 2 pseudo-dominant ones, were recruited. A total of 144 known genes of inherited retinal diseases were selected for deep exome resequencing. Through systematic data analysis using established bioinformatics pipeline and segregation analysis, a number of genetic variants were released. Eleven mutations, eight of them were novel, in the USH2A gene were identified. Biparental mutations in USH2A were revealed in 2 families with pseudo-dominant inheritance. A proband was found to have triple mutations, two of them were supposed to locate in the same chromosome. In conclusion, this study revealed the genetic defects in the USH2A gene and demonstrated the robustness of targeted exome sequencing to precisely and rapidly determine genetic defects. The methodology provides a reliable strategy for routine gene diagnosis of USH.

Figure 1. Families with Usher syndrome.

Pedigrees of the Usher syndrome in this study. Closed symbol represents affected patient and open symbol indicates unaffected subject. The bar over the symbol indicates examined subjects in this study. Arrow indicates proband. Slash represents deceased person. The box labeled with different color indicates different mutation in each pedigree.

Figure 2. Clinical examination.

A. OCT examination demonstrated thinned retina in the proband patient with Usher syndrome (F3-III-15); B. ERG testing showed extinguished rod response; C. representative fundography of the patient.

Figure 3. Mutation spectrum in the USH2A gene.

Gene level overview of the summarized USH2A mutations. The gene is comprised of 71 exons which harbored 1000 distinct mutations so far have been reported. The new identified mutations are marked as arrows in the schema. Each color of the box in the figure represents a mutation type: orange, nonsense mutation; black, splice site mutation; green, indel; pink, frameshift mutation; sky blue, mutation in 3′UTR; blue, intronic mutation; purple, missense mutation. Red asterisk indicates novel mutation discovered in this study. Het-one, single heterozygous mutation; homo, homozygous mutation.