Targeted RNA Test Enhances Genetic Diagnosis in Exome Sequencing

Clinical exome sequencing can identify disease-causing variants but often returns variants of uncertain significance that leave patients without definitive answers. Determining whether these variants disrupt gene function, particularly through abnormal RNA splicing, remains a persistent challenge in routine diagnostics. A new targeted RNA analysis workflow demonstrates how uncertainty from exome testing can be reduced, enabling more genetic disease diagnoses.

ExomeReveal RNA testing from Ambry Genetics (Aliso Viejo, CA, USA), a clinical genomic testing company and wholly owned subsidiary of Tempus AI, Inc., is part of a multiomics exome sequencing approach described in peer-reviewed research published in Genetics in Medicine Open. Combined with exome sequencing, the workflow applies variant-specific RNA analysis to evaluate suspected spliceogenic effects. By examining genes expressed in blood, the method enables transcript-level assessment that can help clarify ambiguous DNA-based findings.

Image: The study shows how targeted RNA analysis with Ambry’s ExomeReveal workflow can resolve uncertain findings and improve diagnostic clarity (Image Credit: iStock)

In the study, researchers reviewed nearly 2,000 unique genetic variants identified through exome sequencing over five years. Approximately one in ten variants were suspected to affect RNA splicing, and more than two‑thirds of these occurred in genes expressed in blood, making them suitable candidates for RNA analysis. Ultimately, about 8% of all variants qualified for additional RNA testing, with more than one‑third of those initially classified as variants of uncertain significance.

A subset of participants consented to follow‑up RNA testing. Among individuals who had received uncertain results, targeted RNA analysis upgraded the variant classification to provide a diagnosis. The authors report that integrating RNA testing into diagnostic pipelines is both achievable and impactful for spliceogenic variants. They also propose criteria to determine which variants are most likely to benefit from RNA testing, offering practical guidance for adoption across clinical laboratories.

“Families deserve clear answers, not uncertainty,” said Tom Schoenherr, CEO of Diagnostics at Tempus. “This study shows that combining exome sequencing with targeted RNA testing offers that possibility to many patients who might otherwise be in limbo. These findings, which have critical implications for improved patient care, demonstrate the meaningful impact we believe modern diagnostics should deliver.”

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