Dual Diagnoses in Pediatric Exomes

Evidence

This retrospective study evaluated 872 unrelated children with suspected genetic disorders at the Department of Pediatrics at the First Affiliated Hospital of Henan University of Chinese Medicine between January 2019 and February 2025. Participants received proband- or trio-based whole-exome sequencing (WES), and 14 children were confirmed to have dual molecular diagnoses. [pmid:42764371]

The investigators defined a dual molecular diagnosis as two pathogenic or likely pathogenic variants, each corresponding to a distinct genetic disease. Phenotypes were standardized with the Human Phenotype Ontology and reviewed by two clinical geneticists. Variant analysis aligned quality-controlled sequencing data to GRCh37/hg19 and assessed single-nucleotide variants, small insertions and deletions, and copy-number variants; variant classification followed American College of Medical Genetics and Genomics standards. [pmid:42764371]

Of 872 WES-tested patients, 370 (42.4%) received a molecular diagnosis, including 14 (3.8%) with dual molecular diagnoses. This percentage is reported in relation to the molecularly diagnosed group in the study’s summary and in relation to the WES-tested cohort in the results description; it should therefore be read as a study-specific diagnostic-frequency finding rather than an estimate of frequency in all pediatric patients with suspected genetic disease. [pmid:42764371]

Sequencing used the IDT xGen Exome Research Panel v2.0 and the BGI-T7 platform, with reported sequencing depth of at least 100×. The workflow also used peripheral-blood DNA from patients and selected family members, principally parents. These design details describe the laboratory and analytical approach used to identify the reported diagnoses. [pmid:42764371]

Analysis — Diagnostic interpretation

The central contribution of this single-study report is its focus on children whose clinical presentation could reflect more than one inherited condition. The reported dual-diagnosis definition required two independently disease-relevant findings rather than a broader collection of uncertain variants. That framing makes the result clinically interpretable at the diagnostic level: the authors were describing cases in which each qualifying variant was considered to explain part of the phenotype, not simply reporting multiple genomic observations from exome testing. [pmid:42764371]

The observed finding of 14 dual diagnoses among 370 molecularly diagnosed patients shows that an explanatory model limited to one gene may be insufficient for some children in this referral cohort. WES was positioned as a first-tier screening approach for complex, multisystemic, or atypical overlapping phenotypes, and its analysis workflow included several variant classes. The study therefore supports considering whether distinct molecular findings may contribute to different elements of a complex presentation when WES data are interpreted in an appropriate clinical context. [pmid:42764371]

The result does not establish that WES will provide the same diagnostic yield or dual-diagnosis frequency in another care setting. The cohort was drawn from one pediatric department, was retrospectively analyzed, and consisted of children already suspected of having genetic disorders. Its reported proportions describe the tested population and the study’s diagnostic process; they do not by themselves compare WES with another test, demonstrate patient benefit, or determine how often dual diagnoses occur outside this cohort. [pmid:42764371]

The methods strengthen the descriptive value of the report by combining structured phenotype review, proband or trio sequencing, and ACMG-guided classification. Still, identification of two pathogenic or likely pathogenic findings is not equivalent to resolving every phenotype-genotype relationship. The authors specifically noted that some associations need further experimental validation, so the report is best read as evidence of diagnostic characterization rather than functional proof of how paired variants interact. [pmid:42764371]

Limitations

The authors identified a small dual-diagnosis case series of 14 children and stated that this sample size may constrain generalizability. They also reported that functional implications of the variants had not been verified in vitro and that some phenotype-genotype associations require additional experimental validation. These limitations restrict conclusions about biological mechanisms and applicability beyond the studied cohort. [pmid:42764371]

No comparative effectiveness outcome, confidence interval, p-value, sensitivity, specificity, or clinical-outcome measure is located in the cited excerpts. Accordingly, the report supports characterization of diagnostic findings in this retrospective cohort, but not conclusions about comparative test performance, clinical utility, or downstream outcomes. [pmid:42764371]