Next generation sequencing-based genetic testing reveals key diagnostic contribution by copy number variants in inherited retinal diseases

Abstract

Purpose : Inherited retinal dystrophies (IRDs) are clinically and genetically diverse disorders, with a wide spectrum of causative genetic variation encompassing sequence alterations, copy number variants (CNVs) and other types of structural variants (SV). An understanding of the diagnostic significance of these different variation types is essential to maximize diagnostic yield in IRDs and select targeted therapies. Therefore, this study aimed to evaluate the rates and characteristics of CNVs, and the role of SVs caused by transposable elements, in a large RD cohort tested using a comprehensive next generation sequencing (NGS)-based RD panel.

Methods : 4581 patients referred for genetic testing between May 2017 and June 2019 were tested using an NGS panel covering 188 or 266 IRD-associated genes. Sequencing was by targeted OS-Seq on the Illumina NextSeq500 platform, or the IDT xGEN Exome Research Panel on the Illumina NovaSeq platform. CNVkit, an in-house developed deletion caller and IGV software were used to detect CNVs and transposable element-related SVs.

Results : A CNV in a gene consistent with the patient’s phenotype was reported in 4.8% of cases. The majority (90%) of CNVs were deletions, while the remaining 10% were copy number gains. Of all CNVs detected, 29% were single exon deletions, while 20% were 2-exon deletions, 28% partial gene deletions (>2 exons) and 14% whole gene deletions. CNVs were identified in 53 genes in total. USH2A and PRPF31 were enriched in CNVs compared to other genes (21% and 8.5% of all deletions respectively). Deletions were also detected in genes for which diagnostic gross deletions are not typically reported, such as ABCA4 and RPE65. The CHM and EYS genes were notable for the number of duplications detected (18% and 13.6% of all copy number gains respectively). In addition, we detected transposable element-related SVs including diagnostic Alu insertions in MAK, USH2A, CRB1 and CEP290, and a novel retrotransposon insertion in CHM.

Conclusions : Genetic testing incorporating high resolution CNV detection in a large cohort of RD patients reveals a key diagnostic contribution by CNVs. Our data demonstrates a significant contribution by single exon deletions, which are technically challenging to detect. Moreover, we present cases with diagnostic transposable elements, further broadening the landscape of genetic variation in IRD.

This is a 2020 ARVO Annual Meeting abstract.