Evaluation of founder effect burden on recurrent variants in X-linked retinoschisis

Abstract

Purpose : Pathogenic variants in the RS1 gene cause X-linked retinoschisis (XLRS), a rare inherited disease that results in childhood vision loss. Variants may be transmitted through multiple generations of unaffected carrier females before an affected male is discovered. Notably, certain RS1 variants are repeatedly reported in seemingly unrelated probands. Here, we investigate recurrent pathogenic variants to determine whether this phenomenon represents founder alleles or multiple mutation events.

Methods : Patients were consented and blood-derived DNA was obtained for analysis. Three polymorphic short tandem repeat (STR) markers and four single nucleotide polymorphism (SNP) markers surrounding the RS1 gene (~2 cM) were selected. Custom STR primers were designed with 5’6 FAM. Proband DNA was amplified with STR primers by Polymerase Chain Reaction (PCR) and analyzed by capillary electrophoresis. Alleles were called based on marker sizes. SNP markers were analyzed by Sanger sequencing. Visualization of haplotype geographical distribution was mapped by Zone Improvement Plan (ZIP) code using Python.

Results : XLRS probands (n=114) with one of the 13 most prevalent RS1 variants were analyzed. Nine variants (69%) had at least two probands with common variant-specific haplotypes over 7/7 markers (~2 cM). Twelve variants (92%) had two or more probands with shared alleles across at least 3/7 markers bilaterally adjacent to RS1 (~0.4 cM). Eleven variants (85%) demonstrated one or more geographic clusters for probands sharing variant-specific haplotypes. Recurrent variants with shared haplotype showed varying degrees of geographic clustering. Overall, 19 unique haplotypes of at least ~0.4 cM surrounding the RS1 gene comprised 87/114 (76%) of reportedly unrelated probands. Additionally, 65/87 (75%) probands with shared haplotypes of ~0.4 cM or more clustered in specific regions of the United States.

Conclusions : Examination of this large XLRS cohort for common RS1 haplotypes supports that the majority are explained by founder effect rather than multiple equivalent mutation events. This is beneficial for clinical variant classification and may be generalizable to other X-linked disorders.

This is a 2021 ARVO Annual Meeting abstract.