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.

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.…”

“…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. 7,10 Despite success in previous studies, there is still a large proportion of patients with IRD who have unidentified genetic mutations. 2 In addition, there are few thorough studies of the relationship between specific genotypes and phenotypes.…”

Olfaction in Parkin carriers in Chinese patients with Parkinson disease

“…The genetic analysis was carried out by target sequencing and multiple ligation‐dependent probe amplification (MLPA) as previously reported (Huang et al., 2013). Briefly, all exons and their corresponding flanking regions of the genes in the panel were selected as target regions.…”

“…The captured libraries were then sequenced using IlluminaNextSeq500 Sequencer with a sequencing depth of 200 × . The raw data was then compared to the reference sequence provided by Mygenostics Inc by standardized procedures (Huang et al., 2013). …”

Identification of false-negative mutations missed by next-generation sequencing in retinitis pigmentosa patients: a complementary approach to clinical genetic diagnostic testing

“…The three major NGS-based methodologies are targeted exome sequencing (TES), whole-exome sequencing (WES), and whole-genome sequencing (WGS). TES is an accurate, rapid, and cost-effective method for genetic screening, 4,5 and WES is useful for identifying novel disease-related genes, albeit at a higher cost than TES. 6,7 WGS analyzes the entire genome and is especially useful for detecting mutations in noncoding regions, structural variations, and copy-number variations.…”