Novel Mutations Associated With Various Types of Corneal Dystrophies in a Han Chinese Population

Abstract

Aims: To study the genetic spectra of corneal dystrophies (CDs) in Han Chinese patients using next-generation sequencing (NGS). Methods: NGS-based targeted region sequencing was performed to evaluate 71 CD patients of Han Chinese ethnicity. A custom-made capture panel was designed to capture all coding exons and untranslated regions plus 25 bp of intronic flanking sequences of 801 candidate genes for eye diseases. The Genome Analysis Tool Kit Best Practices pipeline and an intensive computational prediction pipeline were applied for the analysis of pathogenic variants. Results: We achieved a mutation detection rate of 59.2% by NGS. Eighteen known mutations in CD-related genes were found in 42 out of 71 patients, and these cases showed a genotype-phenotype correlation consistent with previous reports. Nine novel variants that were likely pathogenic were found in various genes, including CHST6, TGFBI, SLC4A11, AGBL1, and COL17A1. These variants were all predicted to be protein-damaging by an intensive computational analysis. Conclusions: This study expands the spectra of genetic mutations associated with various types of CDs in the Chinese population and highlights the clinical utility of targeted NGS for genetically heterogeneous CD.

Keywords: Han Chinese population; corneal dystrophies; mutations; next-generation sequencing; targeted-region sequencing.

Figure 1

CHST6 mutations identified in this study. (A) Schematic diagram of CHST6 exons. The positions of mutations found in this study were labeled, and novel variants were indicated in red. Number of affected individuals was shown in brackets. (B) Validation of the three novel CHST6 mutations by Sanger sequencing, and representative images of the patients that harbored the novel mutations. (C) 3D homology model changes induced by the p.F55S mutation. Hydrogen bonds were shown as red dashed lines. (D) 3D homology model and surface changes induced by the p.P133R mutation.

Figure 2

TGFBI mutations identified in this study. (A) Schematic diagram of TGFBI protein structure including the four fascilin-like (FAS1 1-4) domains. (B) Representative image and in vivo confocal microscopy (IVCM) examination of the patient that harbored the p.L565H mutation. (C) Validation of the p.L565H mutations by Sanger sequencing. (D) 3D homology model of the TGFBI protein (partial). (E–H) Surface changes caused by the p.L565H or p.L565P mutation. The mutations affected the size of the nearby cavity. F–H is a magnification of the area shown in red rectangle in E.

Figure 3

SLC4A11 mutations identified in this study. (A) Schematic diagram of SLC4A11 exons. (B) Validation of the three novel SLC4A11 mutations by Sanger sequencing. (C) Representative images of the patient that harbored double heterozygous mutations, p.G413R and p.L732fs. (D) 3D homology model changes induced by the missense mutations. Hydrogen bonds were shown as red dashed line.

Figure 4

Mutations in AGBL1 (A–F) and COL17A1 (G–K) that identified in this study. (A) Schematic diagram of AGBL1 exons. The position of the p.R748H mutation was labeled with dashed line. (B) Validation of the AGBL1 p.R748H mutation by Sanger sequencing. (C, D) In vivo confocal microscopy (IVCM) examination of the patient that harbored the p.R748H mutation, shown as the lesions in corneal endothelium. (E, F) 3D homology model changes induced by the AGBL1 p.R748H mutation. (G) Schematic diagram of COL17A1 exons. The position of the p.P1185L mutation was labeled with dashed line. (H) Validation of the COL17A1 p.P1185L mutation by Sanger sequencing. (I, J) IVCM examination of the patient that harbored the p.P1185L mutation, shown as the normal corneal epithelium (I) and lesions in corneal endothelium (J). (K) Surface changes caused by the p.P1185L mutation. The mutation showed blocked entrance of the adjacent cavity. The residue in position 1185 was labeled in red.

Figure 5

Conservation analysis of the nine novel mutations identified in this study.