Haplotype characterization of a large X-linked retinoschisis cohort

Abstract

Purpose : Pathogenic variants in the RS1 gene result in X-linked retinoschisis, a rare childhood retinopathy. Multiple recurrent disease-causing alleles have been observed in unrelated individuals, which may represent ancestral founder alleles. To test this, a large cohort of reportedly unrelated probands with equivalent point mutations were evaluated by haplotype analysis to characterize the landscape of disease-associated RS1 mutation events.

Methods : Polymorphic Short Tandem Repeat (STR) markers along the X chromosome (~102 cM) were selected. Primers were designed with M13 tails on the forward primer and combined with 5’6 fluorescein amidite (FAM) engineered with M13 tails. Polymerase Chain Reaction (PCR) was performed on proband DNA and analyzed using capillary electrophoresis. Alleles were determined based on fragment sizes. For fine mapping, single nucleotide polymorphism (SNP) markers close to the RS1 gene (~4 cM) were selected and analyzed by Sanger sequencing. Haplotypes were visualized using HaploPainter.

Results : XLRS probands (n=67) with one of eight prevalent pathogenic RS1 variants were selected for haplotype analysis. Of the eight variants, five had three or more probands with distinct haplotypes across three STR markers surrounding the RS1 gene (~1.8 cM). These included c.214G>A;p.Glu72Lys (4/17), c.286T>C;p.Trp96Arg (9/9), c.208G>A;p.Gly70Ser (two haplotypes: 3/7 and 3/7), c.574C>T;p.Pro192Ser (two haplotypes: 3/8 and 3/8). For a novel RS1 mutation, c.209G>A;p.Gly70Asp, 3/4 probands shared one haplotype. All three probands are of Latino descent and reported familial origins in Bolivia. Six additional family members were examined using the STR markers and SNPs, refining the shared haplotype to ~2 cM. No shared haplotype was observed among the nine probands with c.305G>A;p.Arg102Gln or the nine probands with c.598C>T;p.Arg200Cys.

Conclusions : In this cohort, seven distinct haplotypes surrounding the RS1 gene were shared among reportedly unrelated probands with the same pathogenic RS1 variant, suggesting that multiple founder mutations exist and span many generations of X-linked inheritance. This finding additionally supports the intolerance of RS1 to missense mutation and may serve as a corroborative assay for clinical diagnostic testing.

This is a 2020 ARVO Annual Meeting abstract.