Diagnostic yield and variant spectrum of whole-exome sequencing in Iranian probands with congenital and early-onset ocular disorders

Abstract

Background Inherited ocular disorders are a leading cause of early-onset visual impairment, particularly in populations with high consanguinity such as Iran, where a substantial proportion of affected individuals remain without a molecular diagnosis after conventional evaluation. We aimed to determine the diagnostic yield and variant spectrum of whole-exome sequencing (WES) in Iranian probands with congenital or early-onset ocular disorders that were genetically unresolved by prior testing. Methods Thirty unrelated probands were recruited consecutively (July–September 2024). Genomic DNA underwent exome capture (Agilent SureSelect V7) and paired-end sequencing (Illumina NovaSeq 6000). Reads were cleaned with SOAPnuke, aligned with BWA-MEM, and variants were called with GATK HaplotypeCaller and DeepVariant, filtered by GATK VQSR, and annotated against public and Iranian-specific databases (GEMIRAN, IRANOM). Variants were classified per ACMG/AMP criteria. Diagnostic yield was defined as the proportion of probands with a causative or candidate variant concordant with phenotype. Results A causative or strong candidate variant concordant with the phenotype was identified in 21 of 30 probands (diagnostic yield 70.0%; 95% CI 50.6–85.3%). Pathogenic or likely-pathogenic variants were found in established genes including ABCA4, USH2A, RP1, CRB1, CEP290, GUCY2D, CYP1B1 and TYR. Among the identified genotypes, 54% were homozygous and 12% hemizygous (X-linked), consistent with consanguinity in 11/30 (36.7%) families; 35% were single heterozygous findings in autosomal-recessive genes, interpreted as incomplete genotypes pending detection of a second allele. Onset was infantile in 73% of probands. Conclusions WES is an effective first-tier test for congenital and early-onset ocular disorders in the Iranian population, resolving roughly 70% of previously undiagnosed probands. Single-allele findings in recessive genes indicate that complementary copy-number and structural-variant analysis, deep-intronic assessment, periodic reanalysis, and reflex whole-genome sequencing are needed to maximise yield and support accurate genetic counselling.