Molecular Diagnostic Testing by eyeGENE: Analysis of Patients With Hereditary Retinal Dystrophy Phenotypes Involving Central Vision Loss

Abstract

METHODS.Patients with Best macular dystrophy (BMD), Doyne honeycomb retinal dystrophy (DHRD), Sorsby fundus dystrophy (SFD), or late-onset retinal degeneration (LORD) were screened for mutations in BEST1, EFEMP1, TIMP3, and CTRP5, respectively. Patients with pattern dystrophy (PD) were screened for mutations in PRPH2, BEST1, ELOVL4, CTRP5, and ABCA4; patients with cone-rod dystrophy (CRD) were screened for mutations in CRX, ABCA4, PRPH2, ELOVL4, and the c.2513G>A p.Arg838His variant in GUCY2D. Mutation analysis was performed by dideoxy sequencing. Impact of novel variants was evaluated using the computational tool PolyPhen.RESULTS. Among the 213 unrelated patients, 38 had BMD, 26 DHRD, 74 PD, 8 SFD, 6 LORD, and 54 CRD; six had both PD and BMD, and one had no specific clinical diagnosis. BEST1 variants were identified in 25 BMD patients, five with novel variants of unknown significance (VUS). Among the five patients with VUS, one was diagnosed with both BMD and PD. A novel EFEMP1 variant was identified in one DHRD patient. TIMP3 novel variants were found in two SFD patients, PRPH2 variants in 14 PD patients, ABCA4 variants in four PD patients, and p.Arg838His GUCY2D mutation in six patients diagnosed with dominant CRD; one patient additionally had a CRX VUS. ABCA4 mutations were identified in 15 patients with recessive CRD. CONCLUSIONS.Of the 213 samples, 55 patients (26%) had known causative mutations, and 13 (6%) patients had a VUS that was possibly pathogenic. Overall, selective screening for mutations in BEST1, PRPH2, and ABCA4 would likely yield the highest success rate in identifying the genetic basis for macular dystrophy phenotypes. Because of the overlap in phenotypes between BMD and PD, it would be beneficial to screen genes associated with both diseases.

Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma

“…Previous ocular genetic studies have identified a recurrent, missense mutation in exon-10 of EFEMP1 (c.1033C>T, p.R345W) associated with Doyne honeycomb retinal dystrophy (DHRD) and/or Malattia Leventinese (MLVT, MIM: 126600) in European and Asian families [ 11 , 20 – 24 ]. Recently, a novel intronic variant of unknown significance in EFEMP1 was reported in a DHRD patient [ 25 ]. DHRD/MLVT is an autosomal dominant retinal disease characterized by radial deposits of basal-laminar drusen [ 26 ].…”

A Report on Molecular Diagnostic Testing for Inherited Retinal Dystrophies by Targeted Genetic Analyses

“…followed by dideoxy sequencing and analysis using ABI PRISM 3100 Genetic Analyzer (Applied Biosystems, Foster City, CA) as previously described (Alapati et al, 2014). Mutations, including substitutions, deletions, and insertions, involving a few base pairs in the coding region and splice junctions can be detected with our methodology.…”

Retinal dystrophies and variants in PRPH2

“…This was previously reported in a patient whose pattern dystrophy was classified as "probably damaging" based on in silico analysis determined by PolyPhen2. The absence of this variant in the population databases (1000 genomes, ExAC, and gnomAD), in silico analyses indicating its possible pathogenicity (PolyPhen2, SIFT, MutationTaster, M-CAP, and CADD), change of highly conserved residues, and two new patients with this missense variant (patient 3 and her sister) all reinforce the idea that the p.Arg195Gln variant is probably pathogenic (10) .…”