Diagnostic and clinical utility of exome sequencing and chromosomal microarray in children with GDD/iD: a meta-analysis

Global developmental delay/intellectual disability (GDD/ID) is among the most common neurodevelopmental disorders, with up to half of cases are attributed to genetic factors. Chromosome microarray (CMA) has traditionally been the primary genetic test for idiopathic GDD/ID. However, whole exome sequencing (WES) and whole genome sequencing (WGS) have recently emerged, substantially increasing diagnostic yields in these populations. We conducted a comprehensive literature search of PubMed, Scopus, EMBASE, and the Cochrane Library from inception to April 29, 2025. Studies reporting the diagnostic utility of these tests in children with GDD/ID were included and analyzed. A total of 102 studies, comprising 55,752 children, were reviewed. The pooled diagnostic yield of WES was 0.37 (95% CI: 0.33–0.41; I² = 93%), significantly higher than that of CMA at 0.19 (95% CI: 0.16–0.21; I² = 95%). Subgroup analyses showed that WES yielded significantly higher diagnostic rates than CMA in both same-sample comparisons (OR = 2.27, 95% CI: 1.08–4.78) and different-sample comparisons (OR = 1.65, 95% CI: 1.15–2.37). Only one study evaluated WGS, reporting a diagnostic yield of 0.27. Meta-regression revealed a significant association between CMA diagnostic yield and the proportion of male participants (<i>p</i> &lt; 0.01), but not with WES. No significant difference in diagnostic utility was observed between isolated GDD/ID and GDD/ID with comorbidities. In children with unexplained GDD/ID, WES demonstrates superior diagnostic and clinical utility compared to CMA. Incorporating WES as a first-line investigation in the diagnostic evaluation of GDD/ID may be warranted. The pooled diagnostic yield of whole exome sequencing (WES) was 0.37 (95% CI: 0.33–0.41), significantly higher than that of chromosomal microarray (CMA) at 0.19 (95% CI: 0.16–0.21) in children with global developmental delay/intellectual disability (GDD/ID).No significant difference in diagnostic utility was observed between isolated GDD/ID and GDD/ID with comorbidities.WES may be warranted as a first-line investigation in the diagnostic evaluation of GDD/ID. The pooled diagnostic yield of whole exome sequencing (WES) was 0.37 (95% CI: 0.33–0.41), significantly higher than that of chromosomal microarray (CMA) at 0.19 (95% CI: 0.16–0.21) in children with global developmental delay/intellectual disability (GDD/ID). No significant difference in diagnostic utility was observed between isolated GDD/ID and GDD/ID with comorbidities. WES may be warranted as a first-line investigation in the diagnostic evaluation of GDD/ID.