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

Maliwan Tengsujaritkul·Orawan Louthrenoo·Narueporn Likhitweerawong·Nonglak Boonchooduang·Manit Srisurapanont
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Abstract

BACKGROUND: 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. METHODS: 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. RESULTS: 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 (p&#x2009;<&#x2009;0.01), but not with WES. No significant difference in diagnostic utility was observed between isolated GDD/ID and GDD/ID with comorbidities. CONCLUSION: 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.

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HumansExome SequencingChildDevelopmental DisabilitiesIntellectual DisabilityGenetic TestingMaleMicroarray AnalysisWhole Genome SequencingFemaleDiagnostic yieldexome sequencinggenetic testingglobal developmental delayintellectual disabilityJournal ArticleMeta-AnalysisSystematic ReviewResearch Support, Non-U.S. Gov't

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Maliwan Tengsujaritkul, Orawan Louthrenoo, Narueporn Likhitweerawong, Nonglak Boonchooduang, Manit Srisurapanont. 2025-12-30. Diagnostic and clinical utility of exome sequencing and chromosomal microarray in children with GDD/iD: a meta-analysis.. https://doi.org/10.1080/07853890.2025.2609424

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