Exome analysis revealed novel and known mutations in Indian, Pakistani and Caucasian pedigrees with recessive retinal degeneration

Abstract

Purpose: To identify causative mutations in six unrelated familial cases of autosomal recessive retinal degeneration

Methods: A detailed ophthalmic evaluation including measurement of visual acuity, perimetry, color vision testing, fundus examination, and ERG was performed. Medical and family records were reviewed for the affected members. Blood samples were collected from all available members and DNA was isolated using standard protocol. Exomes of probands were captured using Nimblegen V3 or Agilent V5+UTR kits, and sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and analyzed using GATK algorithms. Variants detected were analyzed by exomeSuite using an autosomal recessive model. Segregation and ethnicity matched control sample analyses were performed by Sanger sequencing.

Results: Six families (4-10 members in each pedigree) with 1-3 affected members were enrolled. Affected members were diagnosed with non-syndromic retinal degeneration. Analysis of sequence variants in probands using exomeSuite detected 6 novel and 4 known mutations. A novel frame shift mutation in CERKL causing premature truncation of protein was found in one pedigree of Indian origin. In a Pakistani pedigree, a previously reported homozygous mutation was detected in the ABCA4 gene. Recessive compound heterozygous causative variants were observed in the remaining four Caucasian pedigrees. One of these, a pedigree from Brazil showed a novel damaging missense and a novel frame shift variant in the RPE65 gene. In a second Caucasian pedigree, two heterozygous nonsense changes (novel and reported) in PDE6B were detected. In two additional pedigrees causative changes were detected in the USH2A and ABCA4 genes. A novel nonsense and a novel damaging missense variant were detected in the USH2A gene in the fifth pedigree. The two ABCA4 variants, one being missense and the other intronic, have been reported previously. All these variants segregated with disease and the novel variants were not detected in ethnicity-matched controls.

Conclusions: Analysis of exome variants in six pedigrees revealed novel and reported homozygous or compound heterozygous mutations in the CERKL, ABCA4, RPE65, PDE6B, and USH2A. These results suggest that the underlying cause of retinal degeneration due to the involvement of mutations in known genes can be determined by sequencing the exome of probands.

Keywords: 539 genetics