Abstract
Purpose :
EYS and USH2A are two of the most common genes that result in autosomal recessive retinitis pigmentosa (arRP) in Taiwanese. However, through next-generation sequencing (NGS) analysis, many RP patients are only found with a single nucleotide variant (SNV) in one allele and the other variant is still unknown. We hypothesize that the other variant may cause by structure variation (SV) and develop the SV detection pipeline.
Methods :
Thirty-five probands performed with a probe-capture-based NGS retinal dystrophy panel which contains 233 related genes and diagnosed with only one SNV in either EYS (18 probands) or USH2A (17 probands) were included. The SVs pipeline combines six detection tools, Manta, Delly, GRIDSS, svaba, DECoN, and CODEX2, because of different approaches for calling SVs and copy number variations (CNVs). The variants called by at least two detection tools were seen as true positive and further validated by amplifying the breakpoints of the structural variant or droplet digital PCR (ddPCR).
Results :
Eight of the 35 probands (23%) were diagnosed with structure variation. Four probands possess large gene deletions in EYS that cause loss of 2-10 exons which are located in the protein N-terminus, among them, the structural variant for 284 kbp deletion was identified in two unrelated individuals which suggests that this variant may be inherited by generation. In USH2A, three probands were found with large deletions that lead to 1-14 exons loss and one proband carried simultaneously large duplication in the region of exon13 to exon14, and deletion in exon13 and flanking area.
Conclusions :
In our observation, analysis of SVs and CNVs could help almost a quarter of partially diagnosed cases of EYS- and USH2A-related RP. These findings urged that SVs and CNVs detection should be included in the regular analysis, especially for highly suspected arRP or autosomal recessive inherited retinal degeneration but partially solved or unsolved patients.
This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.