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

TL;DR

Exome sequencing provides higher diagnostic rates than chromosomal microarray for children with global developmental delay or intellectual disability.

Contribution

This meta-analysis demonstrates that whole exome sequencing outperforms chromosomal microarray in diagnosing GDD/iD in children.

Findings

WES has a pooled diagnostic yield of 0.37, significantly higher than CMA's 0.19.

WES showed higher diagnostic rates in both same-sample and different-sample comparisons.

WES may be recommended as a first-line diagnostic test for GDD/ID.

Abstract

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 (p < 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.

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