Philadelphia, April 15, 2026 – Researchers from Children’s Hospital of Philadelphia (CHOP) developed a new RNA sequencing strategy that can reveal how genetic variants disrupt gene function and improve the diagnosis of rare diseases. In a study published today in the journal Science Advances , the study team demonstrated that this platform could reveal disease-causing genetic variants and provide molecular diagnoses for previously undiagnosed patients, including five individuals whose conditions had remained unresolved after standard testing.
Exome and genome sequencing are widely used methods for identifying genetic variants responsible for rare diseases. However, these approaches have a diagnostic yield of only 20% to 50%, meaning that more than half of patients with suspected rare diseases are unable to obtain a molecular diagnosis. Many genetic variants cause disease by disrupting how RNA molecules are transcribed and processed, meaning their effects cannot always be understood from DNA sequence alone. As a result, researchers and clinicians are increasingly turning to RNA sequencing to better interpret how genetic variants alter gene activity and function and cause disease.
“RNA is a powerful modality for the diagnosis of rare diseases,” said lead senior author Yi Xing, PhD , Associate Chief Scientific Officer for Omics, Technology & Engineering and Francis West Lewis Chair in Computational and Genomic Medicine at CHOP. “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.”
Traditional RNA sequencing methods fragment RNA molecules before sequencing, making it difficult to reconstruct full-length RNA molecules and link disease-associated variants with abnormal RNA processing events across the same molecule. In contrast, long-read RNA sequencing can directly sequence full-length RNA molecules end-to-end, offering the potential to transform RNA-guided interpretation of genetic variants. However, several challenges, including accuracy, cost, and scalability, have limited the widespread use of long-read RNA sequencing for rare diseases to date.
To address these barriers, researchers at CHOP developed STRIPE (Sequencing Targeted RNAs Identifies Pathogenic Events), a targeted long-read RNA sequencing strategy that enables deep sequencing of full-length RNA molecules for any customized disease-specific gene panel.
STRIPE builds upon prior work at CHOP developing TEQUILA-seq , a scalable and low-cost technology for sequencing full-length RNA molecules.
“TEQUILA-seq was designed to make targeted long-read RNA sequencing cost-effective and scalable,” said co-senior author Lan Lin, PhD , assistant professor of Pathology and Laboratory Medicine at CHOP and developer of the TEQUILA-seq technology. “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.”
To evaluate STRIPE, researchers applied the platform to two groups of rare diseases that are extensively studied at CHOP – congenital disorders of glycosylation (CDG) and primary mitochondrial diseases (PMD). These disease classes include many genetically diverse conditions, with new disease-causing variants continuing to be discovered, making them well suited to assess the effectiveness of STRIPE.
“A major challenge in RNA-guided rare disease diagnostics is that disease-relevant tissues are often difficult to obtain from patients,” said co-senior author Rebecca Ganetzky, MD , an attending physician and clinical geneticist in the Mitochondrial Medicine Program at CHOP. “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.”
“This was a mutually beneficial collaboration in which STRIPE’s new CDG diagnoses could be validated due to the measurable disruption these patients exhibit in glycosylation and thus prove their technology,” said co-senior author Andrew C. Edmondson, MD, PhD , founding Director of the CDG Clinic and an attending physician with the Division of Human Genetics at CHOP. “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, ending their diagnostic odyssey and facilitating them access to appropriate clinical care.”
The researchers applied STRIPE to 88 individuals across the two disease groups and healthy controls. The platform accurately re-identified known disease-causing variants and revealed the often complex and sometimes unanticipated consequences of these variants at the RNA level. Importantly, STRIPE clarified the role of previously identified variants with uncertain significance and uncovered new disease-causing variants in five previously undiagnosed patients, enabling clinicians to establish molecular diagnoses that had been elusive.
Since its development, STRIPE has been used to analyze more than 500 patients across multiple clinical programs at CHOP, demonstrating its real-world potential and scalability for rare disease diagnostics.
“By directly revealing how genetic variants disrupt RNA molecules, STRIPE provides a bridge from genetic diagnosis to disease mechanism to targeted therapies,” Xing said. “More broadly, this work reflects a long-standing effort to interpret genetic variants at the level of full-length RNA molecules, and we believe STRIPE can serve as a foundation for RNA-based precision medicine in rare diseases, linking precision diagnostics to precision therapeutics.”
This study was supported by the National Institutes of Health grants R01DK099551, R01GM088342, R01GM121827, R35GM134863, R35GM151098, R35GM158057, R56HG012310, T32HG000046, and U54NS115198, and The Rocket Fund. This work was also supported by institutional programs at CHOP, including the Omics Initiative, Pathology Diagnostic Innovation Fund, Cell and Gene Therapy Collaborative, and Frontier Programs. CHOP has filed a patent application for the STRIPE technology.
Wang et al, “Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation.” Sci Adv . Online April 15, 2026. DOI: 10.1126/sciadv.ady9895.
About Children’s Hospital of Philadelphia:
A non-profit, charitable organization, Children’s Hospital of Philadelphia was founded in 1855 as the nation’s first pediatric hospital. Through its long-standing commitment to providing exceptional patient care, training new generations of pediatric healthcare professionals, and pioneering major research initiatives, the hospital has fostered many discoveries that have benefited children worldwide. Its pediatric research program is among the largest in the country. The institution has a well-established history of providing advanced pediatric care close to home through its CHOP Care Network , which includes more than 50 primary care practices, specialty care and surgical centers, urgent care centers, and community hospital alliances throughout Pennsylvania and New Jersey. CHOP also operates the Middleman Family Pavilion and its dedicated pediatric emergency department in King of Prussia, the Behavioral Health and Crisis Center (including a 24/7 Crisis Response Center) and the Center for Advanced Behavioral Healthcare , a mental health outpatient facility. Its unique family-centered care and public service programs have brought Children’s Hospital of Philadelphia recognition as a leading advocate for children and adolescents. For more information, visit https://www.chop.edu.
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Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation
15-Apr-2026