The Issue: Patient-X, a pediatric case, presented with developmental delay, epilepsy, hypotonia, craniofacial dysmorphism, pulmonary hypertension, artial septal defect and microcephaly. Standard initial genomic testing, including chromosomal microarray (CMA) and whole exome/genome sequencing (WES/WGS), identified a chromosome 2 deletion but failed to provide meaningful interpretation. The analysis was limited to select gene annotations, offering no clear connection between the variant and the patient’s phenotype. As a result, the family was left without a diagnosis, actionable insights, or a clear care pathway.

Genoxus Approach: Genoxus reanalyzed the case using a more comprehensive, data-centric approach. Instead of focusing on isolated genes, the entire deletion region was examined using Genoxus Annotation™, a cloud-based, SQL-queryable platform integrating multi-source genomic evidence, including ClinVar, alongside phenotype-driven analysis. This broader methodology enabled deeper genotype-phenotype correlation beyond conventional pipelines.

The Discovery: The reanalysis uncovered a strong association with 2q32-q33 deletion syndrome and SATB2 associated disorder, linking the chromosome 2 deletion to key clinical features, including developmental delay, hypotonia, craniofacial anomalies, and autism-related behaviors—connections missed in the original report.

The Impact: This insight guided targeted follow-up, leading to a confirmed autism diagnosis and a more precise care plan. Genoxus did not generate new data—it revealed the clinical meaning already embedded within it, transforming fragmented results into actionable clarity.