ARRP microarray and Exome analysis revealed known and novel mutations in Mexican pedigrees.

Abstract

Purpose: To identify possible causative mutations in four unrelated families with autosomal recessive retinal degeneration.

Methods: Clinical analysis included full ophthalmic exam, refraction, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, Ocular coherent tomography, fluorescein angiography and color vision test. Blood samples were collected from affected and unaffected family members and DNA isolated using standard protocol. DNA was analyzed for known mutations using Asper arRP and arLCA array. In addition, exome of one proband was captured using Nimblegen V3, and sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were identified using GATK. Variants detected in these individuals were analyzed by exomeSuite using an autosomal recessive model. Segregation and ethnicity matched control sample analysis were performed by Dideoxy sequencing.

Results: Four families comprising 3-6 in each pedigree with 1-3 affected members were recruited from Yucatan Peninsula, Mexico. Affected members were diagnosed with LCA and cone/rod dystrophy and RP-Usher type. A homozygous missense change p.C759F segregating with disease was found in the USH2A gene in one of the pedigrees. This change was previously described in other patients. In a second pedigree another previously described homozygous change p.P575L in GUCY2D segregating with disease was observed. In the third pedigree compound heterozygous mutations, p.G104V and p.R124* in the gene RPE65 were observed to segregate with retinal degeneration. Analysis of exome sequence variants observed in the proband of the fourth pedigree detected one novel homozygous missense, potentially pathogenic change p.D2102E in the ABCA4 gene. Analysis of 100 ethnicity-matched controls did not detect the presence of the novel ABCA4 change indicating that this is a rare variant in Mexican population.

Conclusions: Analysis of 15 patients from Mexico for known mutations identified previously reported mutations in the USH2A, GUCY2D and RPE65 genes. Exome sequencing of the proband of one pedigree reveled a novel homozygous mutation in the ABCA4 gene. In summary, screening patients with a diagnosis of LCA, RP, Usher syndrome, cone/rod dystrophy from Mexico identified four previously described mutations and one novel mutation in genes implicated in causing recessive retinal dystrophies.