Researchers at Children's Hospital of Philadelphia (CHOP) announced on Apr. 15 the development of a new RNA sequencing strategy designed to improve the diagnosis of rare diseases. The study, published in Science Advances, shows that this approach can reveal how genetic variants disrupt gene function and provide molecular diagnoses for patients who previously lacked answers after standard testing.
The need for improved diagnostic tools is significant because exome and genome sequencing currently only provide answers for about 20% to 50% of patients with suspected rare diseases. Many disease-causing genetic variants impact RNA processing in ways that cannot be fully understood from DNA sequence alone, prompting researchers to seek better methods such as RNA sequencing.
Traditional RNA sequencing fragments molecules before analysis, making it difficult to connect genetic variants with abnormal processing events. Long-read RNA sequencing can sequence full-length molecules but has faced challenges related to accuracy, cost, and scalability. To address these issues, CHOP researchers developed STRIPE (Sequencing Targeted RNAs Identifies Pathogenic Events), a targeted long-read strategy allowing deep analysis of any customized gene panel relevant to specific diseases.
Lan Lin, PhD, assistant professor at CHOP and developer of TEQUILA-seq technology upon which STRIPE builds, 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." Co-senior author Rebecca Ganetzky, MD added: "STRIPE enables high-quality analysis of RNA from clinically accessible tissues such as skin fibroblasts and blood while still capturing the disease-relevant signals needed to interpret the RNA-level effects of genetic variants." Andrew C. Edmondson, MD emphasized the collaborative benefits: "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..."
The team applied STRIPE in two groups—congenital disorders of glycosylation (CDG) and primary mitochondrial diseases (PMD)—analyzing samples from 88 individuals plus healthy controls. The platform accurately identified known pathogenic variants and clarified uncertain cases while uncovering new diagnoses in five previously unresolved patients.
Since its introduction at CHOP clinics across multiple programs—with over 500 patient analyses—STRIPE has demonstrated potential for broader use in rare disease diagnostics. Xing said: "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..."
The study received support from several National Institutes of Health grants as well as institutional programs at CHOP.
