Identification of pathogenic mutations in patients with inherited retinal dystrophies using whole genome sequencing

Abstract

Purpose : To identify the genetic basis for disease in patients affected with inherited retinal dystrophies (IRD).

Methods : Blood samples were collected from members of families in which pathogenic mutations had not been identified. Whole genome sequencing (WGS) of affected and unaffected family members was performed using Illumina HiSeq X10. Sequence reads were aligned to hg19 using BWA-MEM and variant calling was performed using GATK. Variants were annotated with SnpEff v4.11, PolyPhen v2.2.2, and CADD v1.3. Copy number variations (CNVs) were called using Genome STRiP (svtoolkit 2.00.1611) and SpeedSeq software. Variants were filtered to detect rare, potentially pathogenic variants segregating with disease. Segregation of candidate variants was tested in all available members by Sanger sequencing. Clinical phenotype data of patients with IRD, including ophthalmic examination, electroretinography, visual field testing, fundus photography, and pedigree analysis was reviewed.

Results : The results presented here are part of a larger ongoing study to screen families affected with IRD. In total, we screened 22 families and pathogenic or likely pathogenic variants were found in 19 families. The results of 4 families affected with IRD are reported here. One to four members from each family were included in the WGS. On average, 4 to 6 million SNVs were identified in each family. After filtering, 2 to 9 possible disease-causing variants were identified. Among these, deletions in RPGR and CERKL, a nonsense change in CERKL, a single nucleotide duplication in PDE6G, and a missense change in CRX were found to segregate with disease in 4 unrelated families. Of note, the patient with the RPGR mutation was affected with retinitis pigmentosa (RP) and a Coat’s like neovascularization, which is uncommon in patients with XLRP. The family with the duplication in PDE6G is only the second family to have been reported with likely pathogenic variants in this gene and the only one reported to date with a congenital stationary night blindness phenotype. The phenotype from the other two families matched with previous genotype-phenotype correlations: one had autosomal dominant RP (CRX mutation) and the other autosomal recessive Cone-Rod Dystrophy (CERKL mutations).

Conclusions : Performing WGS is an effective method for identifying the underlying genetic basis for disease in patients affected with IRD.

This is an abstract that was submitted for the 2017 ARVO Annual Meeting, held in Baltimore, MD, May 7-11, 2017.