Researchers at Children’s Hospital of Philadelphia (CHOP) announced on Apr. 16 the development of a new RNA sequencing strategy that aims to improve the diagnosis of rare diseases. The study, published in Science Advances, describes how this platform was able to identify disease-causing genetic variants and provide molecular diagnoses for patients who previously remained undiagnosed after standard testing.
The issue is significant because traditional exome and genome sequencing methods only yield a diagnosis in about 20% to 50% of cases, leaving many patients without answers. Many genetic variants affect how RNA molecules are processed, making their effects difficult to interpret from DNA sequence data alone.
Lead senior author Yi Xing, PhD, Associate Chief Scientific Officer for Omics, Technology & Engineering at CHOP, said: “RNA is a powerful modality for the diagnosis of rare diseases. By directly observing RNA molecules, we can obtain a more complete picture of how genetic variants alter gene products, in ways that DNA sequencing alone cannot reveal.”
The new approach uses STRIPE (Sequencing Targeted RNAs Identifies Pathogenic Events), which allows deep sequencing of full-length RNA molecules tailored to specific disease gene panels. STRIPE builds upon TEQUILA-seq technology developed at CHOP. Co-senior author Lan Lin, PhD said: “TEQUILA-seq was designed to make targeted long-read RNA sequencing cost-effective and scalable. With an RNA-to-data cost of around $100 per sample, STRIPE enables ultra-deep, full-length RNA sequencing of disease-relevant genes at a scale that is practical for clinical applications.”
STRIPE was tested on two groups studied extensively at CHOP—congenital disorders of glycosylation (CDG) and primary mitochondrial diseases (PMD). The platform successfully identified known pathogenic variants and clarified uncertain ones in these conditions using samples from clinically accessible tissues such as skin fibroblasts and blood.
Rebecca Ganetzky, MD said: “A major challenge in RNA-guided rare disease diagnostics is that disease-relevant tissues are often difficult to obtain from patients. STRIPE enables high-quality analysis … while still capturing the disease-relevant signals needed.” Andrew C. Edmondson, MD added: “In turn CDG patients with high unmet diagnostic needs could be given access to a novel technology after current standard-of-care testing had failed and ultimately receive a molecular diagnosis…”
Since its introduction at CHOP programs across multiple clinics have used STRIPE with over 500 patients analyzed so far.
Xing concluded: “By directly revealing how genetic variants disrupt RNA molecules, STRIPE provides a bridge from genetic diagnosis to disease mechanism to targeted therapies … we believe STRIPE can serve as a foundation for RNA-based precision medicine in rare diseases…”
