Identification of causative mutations in ten pedigrees with inherited retinal degeneration by whole genome analysis (WGS)

Abstract

Purpose : Analysis of 10 pedigrees with a diagnosis of IRD to identify the underlying cause of pathology

Methods : DNA isolation was performed on 24 affected and 29 unaffected individuals from 10 pedigrees with IRD. WGS was performed on 21 individuals using Illumina HiSeq X Ten. The sequence alignment and variant calling was done with the Illumina DRAGEN Bio-IT Platform, BWA-MEM+GATK-HC software with high accuracy for both SNPs and INDELs. Annotation of variants included SpliceAI and PrimateAI. Segregation analysis of all identified candidate variants was performed by PCR followed by Sanger sequencing.

Results : The pedigrees analyzed belonged to four different ethnic groups: one each of Ashkenazi Jewish, Hispanic and Pakistani origin, while the remaining 7 are of European American (EA) origin. Our analysis detected 12 pathogenic variants in 9 genes associated with IRD. Two novel compound heterozygous nonsense variants (p.[Glu526*;p.Gln1629*]) segregated with disease in one EA pedigree. A set of known compound heterozygous mutations c.5012+5G>A and p.Arg1752Trp in CEP290 were observed in another EA pedigree. Interestingly, two large structural variants were identified in the PRPF31 gene in two unrelated EA pedigrees. A known heterozygous mutation p.Ser212Gly in the PRPH2 gene segregated with IRD in an EA family with dominant IRD. A novel homozygous variant in DRAM2 (p.Ser234Tyr) and a reported nonsense mutation in RLBP1 (p.Tyr111*) were detected in the remaining two EA pedigrees. A known homozygous CRB1 mutation, p.Arg764Cys was detected in the Pakistani pedigree, while a previously reported nonsense mutation p.Gly723* in RP1 was found in the Ashkenazi Jewish pedigree. In the Hispanic pedigree, a novel intronic homozygous variant c.1107+3A>G in PDE6B was identified as a disease-causing variant.

Conclusions : Our analysis detected 4 novel and 8 previously reported mutations segregating with IRD in 10 pedigrees. These mutations include 4 nonsense, 2 intronic, 4 missense and two large structural changes in ALMS1, PDE6B, CEP290, DRAM2, RLBP1, PRPF31, RP1, PRPH2 and CRB1.

This is a 2021 ARVO Annual Meeting abstract.