Whole Genome Sequencing of an Asian Multi-ethnic Fuchs’ Endothelial Corneal Dystrophy Cohort

Abstract

Purpose : This cross-sectional observational study performed whole genome sequencing (WGS) in a Singaporean cohort to identify variants associated with Fuchs’ Endothelial Corneal Dystrophy (FECD). It also investigated the reliability of WGS to quantify CTG18.1 trinucleotide repeat expansions (CTG-E) within transcription factor 4 (TCF4), versus conventional short tandem repeat (STR) and triplet-primed PCR (TP-PCR) assays. We hypothesised that FECD-associated genetic variants and CTG-E profiles in the Singaporean cohort may differ from cohorts in other countries and ethnicities

Methods : Genomic DNA was extracted from blood samples of 140 FECD patients (120 Chinese, 4 Malay, 8 Indian, 8 other ethnic descent). Control data was derived from 9770 subjects from the SG10K Reference Genome Database. WGS was performed with Illumina TruSeq at 30x coverage. After quality checks, data from 127 FECD and 8246 control participants underwent post-sequencing analysis. Variant analysis and gene burden testing were conducted, focusing on 22 genes chosen based on previous associations with FECD. Potentially damaging variants were identified based on minor allele frequency, disruption of protein-coding sequences and Polyphen-2 prediction scores. CTG-E were also genotyped manually using triplet-primed PCR (TP-PCR) and STR assays

Results : 1732 variants were identified out of the 22 selected genes, of which missense variations comprised the largest proportion (1620/1732). 690 variants (39.84%) were predicted to be damaging. The COL8A2 gene was identified to have strong associations with FECD in the Singaporean cohort. The SLC4A11 gene had significant associations with FECD only in the Singaporean Chinese subgroup. Amongst the other 20 genes, no other variant appeared to be significantly causative for FECD in the Singaporean cohort. 39.3% (55/140) of FECD subjects in Singapore expressed CTG-E. There was 95.7% (134/140) concordance when comparing CTG18.1 genotyping results of WGS against conventional TP-PCR and STR assays

Conclusions : The Singaporean FECD cohort has a lower prevalence of CTG-E than European and North American cohorts. Further studies are required to ascertain genetic and non-genetic causative components in the Singaporean FECD population to tailor a suitable therapeutic strategy. As WGS becomes increasingly accessible and affordable, computational analysis can potentially substitute manual genotyping of CTG18.1

This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.