Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent

Ophthalmic Genet. Jan-Feb 2018;39(1):73-79. doi: 10.1080/13816810.2017.1373830. Epub 2017 Sep 25.

Abstract

Purpose: To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico.

Methods: A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray. The remaining three pedigrees were analyzed using a custom-designed targeted capture array covering the exons of 233 known retinal degeneration genes. Sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were annotated using GATK and filtered by exomeSuite. Segregation and ethnicity-matched control sample analyses were performed by dideoxy sequencing.

Results: Six pedigrees with IRD were analyzed. Nine rare or novel, potentially pathogenic variants segregating with the phenotype were detected in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes. Among these, six were known mutations while the remaining three changes in USH2A, RPE65, and FAM161A genes have not been previously reported to be associated with IRD. Analysis of 100 ethnicity-matched controls did not detect the presence of these three novel variants indicating, these are rare variants in the Mexican population.

Conclusions: Screening patients diagnosed with IRD from Mexico identified six known mutations and three rare or novel potentially damaging variants in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes that segregated with disease.

Keywords: ARRP; LCA; Mexican population; Retinal degeneration; exome sequencing; targeted sequencing.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • ATP-Binding Cassette Transporters / genetics
  • Adolescent
  • Adult
  • Aged
  • Child, Preschool
  • DNA Mutational Analysis
  • Extracellular Matrix Proteins / genetics
  • Eye Proteins / genetics*
  • Female
  • Genetic Determinism
  • Genotyping Techniques
  • Humans
  • IMP Dehydrogenase / genetics
  • Male
  • Mexico / epidemiology
  • Middle Aged
  • Mutation*
  • Pedigree
  • Phenotype
  • Retinal Degeneration / ethnology
  • Retinal Degeneration / genetics*
  • Whole Exome Sequencing
  • cis-trans-Isomerases / genetics

Substances

  • ABCA4 protein, human
  • ATP-Binding Cassette Transporters
  • Extracellular Matrix Proteins
  • Eye Proteins
  • FAM161A protein, human
  • USH2A protein, human
  • IMP Dehydrogenase
  • IMPDH1 protein, human
  • retinoid isomerohydrolase
  • cis-trans-Isomerases