Identification of causative mutations in consanguineous pedigrees from Pakistan with recessive retinal degeneration by whole exome analysis

Abstract

Purpose: To describe the clinical phenotype and identify the causative mutations in four unrelated consanguineous Pakistani families with autosomal recessive retinal degeneration.

Methods: Clinical phenotype in each case was characterized by standard ophthalmic evaluation, fundus photography, electroretinography and optical coherence tomography. Exomes of probands in each pedigree were captured using Nimblegen V4 kits and sequencing was performed on illumina HiSeq. The read mapping, variant calling were performed using published protocols. Variants were analyzed using exomeSuite software to identify candidate genes consistent with the predicted pattern of inheritance. Segregation of candidate mutations in respective families and their evaluation in unaffected Pakistani control subjects was investigated by dideoxy sequencing.

Results: The four large inbred families (5-17 available members in each pedigree) with multiple consanguineous marriages (1-3 per family) and several affected members (3-13 per family) were recruited from Pakistan. Affected members in all four pedigrees were diagnosed with early onset severe non-syndromic retinal degeneration. Analysis of sequence variants in probands of all four pedigrees using exomeSuite and stringent filtering criteria detected 1 or 2 potential candidate genes. A novel variant, c.2384G>A; p.Arg795Gln in GUCY2D that is predicted to be probably damaging by PolyPhen was found in pedigree 1. Similar analysis of pedigree 2 revealed the presence of a novel possibly damaging variant c.2189T>C; p.Phe730Ser in the GUCY2D gene. A previously reported mutation c.1087C>A; p.P363T in the RPE65 gene was detected in pedigree 3 while a single base deletion in the LCA5 gene, c.1151delC (p.Pro384GlufsX18) that was previously reported in a Pakistani family was detected in pedigree 4. All above-mentioned variations were homozygous in affected individuals and segregated with the disease in their respective pedigrees. The novel changes were not observed in 190 ethnicity matched controls.

Conclusions: The exome analysis of samples from 4 pedigrees revealed two novel missense mutations in GUCY2D and previously reported mutations in the RPE65 and LCA5. These results strongly suggest that novel and/or previously reported mutations in genes implicated in retinal disease contribute to early onset retinal degeneration in the Pakistani population.

Keywords: 539 genetics • 696 retinal degenerations: hereditary • 537 gene screening