Genetic analysis of 10 pedigrees with inherited retinal degeneration by exome sequencing and phenotype-genotype association

Abstract

Our purpose was to identify causative mutations and characterize the phenotype associated with the genotype in 10 unrelated families with autosomal recessive retinal degeneration. Ophthalmic evaluation and DNA isolation were carried out in 10 pedigrees with inherited retinal degenerations (IRD). Exomes of probands from eight pedigrees were captured using Nimblegen V2/V3 or Agilent V5+UTR kits, and sequencing was performed on Illumina HiSeq. The <i>DHDDS</i> gene was screened for mutations in the remaining two pedigrees with Ashkenazi Jewish ancestry. Exome variants were filtered to detect candidate causal variants using exomeSuite software. Segregation and ethnicity-matched control sample analysis were performed by dideoxy sequencing. Retinal histology of a patient with <i>DHDDS</i> mutation was studied by microscopy. Genetic analysis identified six known mutations in <i>ABCA4</i> (p.Gly1961Glu, p.Ala1773Val, c.5461-10T>C), <i>RPE65</i> (p.Tyr249Cys, p.Gly484Asp), <i>PDE6B</i> (p.Lys706Ter) and <i>DHDDS</i> (p.Lys42Glu) and ten novel potentially pathogenic variants in <i>CERKL</i> (p.Met323Val fsX20), <i>RPE65</i> (p.Phe252Ser, Thr454Leu fsX31), <i>ARL6</i> (p.Arg121His), <i>USH2A</i> (p.Gly3142Ter, p.Cys3294Trp), <i>PDE6B</i> (p.Gln652Ter), and <i>DHDDS</i> (p.Thr206Ala) genes. Among these, variants/mutations in two separate genes were observed to segregate with IRD in two pedigrees. Retinal histopathology of a patient with a <i>DHDDS</i> mutation showed severe degeneration of retinal layers with relative preservation of the retinal pigment epithelium. Analysis of exome variants in ten pedigrees revealed nine novel potential disease-causing variants and nine previously reported homozygous or compound heterozygous mutations in the <i>CERKL</i>, <i>ABCA4, RPE65</i>, <i>ARL6, USH2A</i>, <i>PDE6B</i>, and <i>DHDDS</i> genes. Mutations that could be sufficient to cause pathology were observed in more than one gene in one pedigree.