Chromosomal Microarray Analysis in Critically Ill Neonates and Children: Diagnostic Yield and Clinical Utility

Chromosomal microarray analysis (CMA) is widely used to detect chromosomal aneuploidies and copy number variants (CNVs) in pediatric patients with congenital anomalies or developmental concerns. However, its diagnostic utility in critically ill neonates and children admitted to intensive care units (ICUs) remains undercharacterized. We conducted a retrospective review of 679 patients admitted to the neonatal, pediatric, or cardiovascular intensive care units (NICU, PICU, CVICU) at Phoenix Children’s Hospital between 2019 and 2024 who underwent CMA. Demographic data, clinical indications, and CMA results were extracted from electronic medical records to assess diagnostic yield and variant patterns. CMA identified a clinically relevant finding in 102 of 679 patients, resulting in an overall diagnostic yield of 15.0% (95% CI: 12.3–17.7%). Clinically relevant findings included pathogenic (P) variants (n = 88), likely pathogenic (LP) variants (n = 12), and large regions of absence of heterozygosity (AOH) consistent with uniparental disomy (UPD) (n = 2). A variant of uncertain significance (VUS) was detected in 139 patients (20.5%). Among the pathogenic and likely pathogenic variants, CMA identified recurrent CNVs (n = 49), nonrecurrent CNVs (n = 17), aneuploidies (n = 22), and patients with two pathogenic or likely pathogenic CNVs (n = 10). Diagnostic yields of 48.4% (95% CI: 38.5–58.4%) and 8.4% (95% CI: 6.0–11.5%) were observed in patients with single or multiple congenital anomalies including a congenital heart defect (CA + CHD), and in patients with an isolated CHD, respectively. CMA demonstrates significant diagnostic value in critically ill neonates and children, particularly among those with multisystem congenital anomalies. These findings support the routine integration of CMA in genomic evaluation protocols for ICU populations to guide diagnosis, management, and counseling.