Whole Exome Sequencing in Pediatric Rare Diseases: Genomic Insights and Clinical Utility from single canter Indian Cohort

<title>Abstract</title> <p>Background Rare genetic disorders are a significant cause of pediatric morbidity and mortality, yet remain underdiagnosed due to genetic heterogeneity and phenotypic overlap. Whole-exome sequencing (WES) has emerged as a powerful diagnostic tool. Objective To determine the diagnostic yield, variant spectrum, and clinical impact of WES in South Asian pediatric patients with suspected genetic disorders. Methods Ninety two probands underwent WES on the Illumina NextSeq 2000 platform following library preparation with the Sophia Genetics kit. Variants were analyzed using SOPHiA DDM, and classified according to Richards S et al, ACMG 2015 guidelines. Pathogenic (P) and likely pathogenic (LP) variants were confirmed by Sanger sequencing. Descriptive statistics were applied to summarize diagnostic yield, inheritance, and variant characteristics. Results Among 92 patients (57 males; 35 females), a molecular diagnosis was achieved in 19 cases (20.65%). Variant classification included: 11 (11.95%) cases reported with pathogenic, 08 (8.69%) cases were likely pathogenic, and 44 (47.85%) cases were reported with variant of uncertain significance (VUS) and 3 cases reported with pathogenic, Likely pathogenic secondary findings. Inheritance patterns were predominantly autosomal dominant heterozygous, followed by autosomal recessive heterozygous, autosomal recessive homozygous, X-linked and mitochondrial, 12 (13%) cases were negative, 14 cases were found autosomal recessive carriers. Clinical indications were dominated by developmental delay &amp; epilepsy, autism and inborn errors of metabolism, primary immunodeficiency, and Other Neurological/Multisystem Manifestations (30, 15, 14, 7 and 26 cases, respectively). Conclusions WES achieved a diagnostic yield of 20.65% in this South Asian pediatric cohort, comparable to international reports. These findings support early integration of WES into clinical workflows and highlight the need for population-specific genomic databases to improve variant interpretation.</p>