Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation

Area of Science:

• Genomics
• Molecular Biology
• Medical Genetics

Background:

• Diagnosing rare genetic diseases is challenging, with current clinical testing limitations.
• Long-read RNA sequencing (RNA-seq) shows promise for variant effect analysis but faces adoption hurdles.
• Existing methods struggle with comprehensive transcript analysis for rare disease diagnosis.

Purpose of the Study:

• To develop and validate STRIPE (Sequencing Targeted RNAs Identifies Pathogenic Events), a targeted long-read RNA-seq strategy.
• To improve the diagnosis and variant interpretation of rare genetic diseases.
• To overcome limitations of current RNA-seq approaches in clinical settings.

Main Methods:

• STRIPE utilizes targeted long-read RNA sequencing for deep sequencing of selected gene panels.
• The strategy enables detection of transcript aberrations and sequence variants at haplotype resolution.
• Applied to 88 individuals across two rare disease groups.

Main Results:

• STRIPE accurately identified known pathogenic variants and their transcript consequences.
• Complex RNA processing defects were observed in splice site variants, including cryptic polyadenylation.
• STRIPE resolved variants of uncertain significance and identified causative variants in five undiagnosed individuals.

Conclusions:

• STRIPE is a powerful, adaptable, and scalable strategy for rare disease diagnosis.
• The method enhances clinical variant interpretation by providing detailed transcript information.
• STRIPE has broad potential to advance the genetic diagnosis of rare diseases.