Inborn errors of metabolism in unexplained early childhood deaths: a retrospective cohort study combining MS/MS and WES

Expanded newborn screening using tandem mass spectrometry (MS/MS) is not universally implemented, and some inborn errors of metabolism (IEMs) may remain undiagnosed in children who die early. We evaluated metabolic and molecular findings among MS/MS-positive cases identified by retrospective analysis of archived neonatal dried blood spots (DBS) from an under-five mortality cohort in Shenzhen, China. We retrospectively reviewed 2,652 under-five deaths recorded in Shenzhen from January 2016 to December 2023. After applying prespecified record-based cause-of-death exclusions and excluding deaths occurring within 72 h of birth, 1,982 children remained eligible for metabolic investigation. Archived neonatal DBS were available for 652 children and analyzed for 43 metabolites by MS/MS. The screening panel targeted 48 conditions using individual metabolite concentrations and prespecified metabolite ratios. All 50 MS/MS-positive cases underwent whole-exome sequencing (WES). Demographic and perinatal characteristics, descriptive IEM proportions by recorded primary abnormal analyte, and metabolite–genotype concordance were analyzed. Fifty cases were MS/MS positive. Thirteen children (13/50, 26.0%) received definitive molecular diagnoses, comprising 12 IEMs (12/50, 24.0%) and one Smith–Magenis syndrome; one additional case was classified as probable ornithine transcarbamylase deficiency (OTCD). The primary comparison included 13 definitively diagnosed cases and 37 cases without a definitive molecular diagnosis. Compared with the latter group, definitively diagnosed cases had lower rates of low birth weight (31% versus 84%, P < 0.001), preterm birth (15% versus 78%, P < 0.001), and obstetric complications (46% versus 78%, P = 0.040). Clear metabolite–genotype concordance was observed in 9/13 (69.2%) definitively diagnosed cases, with partial concordance in 2/13 and non-concordance in 2/13. Retrospective analysis integrating MS/MS and WES identified previously undiagnosed metabolic and genetic conditions among MS/MS-positive cases in a pediatric mortality cohort. MS/MS provided disease-consistent biochemical signals for several classic IEMs, particularly fatty acid oxidation disorders, whereas WES established the molecular diagnoses and clarified atypical, nonspecific, or metabolite–genotype discordant findings. These findings support broader access to expanded newborn MS/MS screening and the risk-stratified use of genomic testing in selected clinically or biochemically unresolved cases. Not applicable.