Completely In-House Targeted Gene Sequencing Reveals Rare Variants Linked to FEVR, Norrie Disease and Persistent Fetal Vascular Syndrome

Document Type

Conference Proceeding

Publication Date

6-2024

Publication Title

Investigative Ophthalmology and Visual Science

Abstract

Purpose : To identify genetic variants in pediatric patients with Familial Exudative Vitreoretinopathy (FEVR), Norrie disease (ND), or Persistant Fetal Vascular Syndrome (PFVS) via a custom Illumina AmpliSeq pediatric retinal disease gene panel. An 20-person cohort of patients diagnosed with FEVR/ND/PFVS and family members was sequenced using a 7-gene panel covering NDP, FZD4, LRP5, TSPAN12, KIF11, CTNNB1, and ZNF408, with variants in NDP associated with ND/PFVS and variants in all 7 genes associated with FEVR.

Methods : An in-house and custom analysis was used without the need of a core DNA-sequencing facility. Blood samples were acquired from pediatric patients and family members seen at Associated Retinal Consultants, PC, (ARC) of Royal Oak, Michigan, USA. Genomic DNA was extracted, followed by creation of Illumina AmpliSeq targeted gene libraries and sequencing with the Illumina iSeq-100. A custom targeted 7-gene panel allowed for full coverage of 83 exons with an additional 25 bp of adjacent intron sequences. VCF files were analyzed via the Ensembl Variant Effect Predictor Database and variant consequences were assessed via ClinVar.

Results : Out of 20 patient samples, 16 patients presented with variants in coding regions, with a total of 35 gene-altering variants within ZNF408, LRP5, TSPAN12 and NDP. A rare ZNF408 missense variant (Ser225Phe) was identified in a female pediatric patient diagnosed with FEVR. The same variant was observed to be present in the patient’s father, but he presents with no retinopathy. Two male patients with ND presented with different novel and rare variants in NDP, with a premature stop codon (Arg37Ter) in one and deletion (Leu13_Met19del) in the other. A novel frameshift mutation induced a premature stop codon (Met32TrpfsTer9) in NDP in another male patient diagnosed with PFVS.

Conclusions : The missense variant (Ser225Phe) in ZNF408 is reported to be of uncertain significance by ClinVar but appears to be extremely rare. The father with the same variant in the absence of FEVR implies that the variant cannot be the sole factor for the daughter's FEVR state. Premature stop codons in NDP (Arg37Ter, Met32TrpfsTer9) render the Norrin protein nonfunctional, and the deletion (Leu13_Met19del) may alter its trafficking signal. Pathogenic variants were found for several families from targeted sequencing of a relatively small cohort of subjects.

Volume

65

Issue

7

First Page

4665

Comments

Association for Research in Vision and Ophthalmology Annual Meeting, ARVO 2024, May 5-9, 2024, Seattle, WA

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