Long read sequencing enhances pathogenic and novel variation discovery in patients with rare diseases

Abstract

Abstract With ongoing improvements in accuracy and capacity to detect complex genomic and epigenomic variations, long-read sequencing (LRS) technologies could serve as a unified platform for clinical genetic testing, particularly in rare disease settings, where nearly half of patients remain undiagnosed using existing technologies. Here, we report a simplified funnel-down filtration strategy aimed at identifying large deleterious variants and abnormal episignature disease profiles from whole-genome LRS data. This approach substantially reduced structural and copy number variants by 98.5–99.9%, respectively, while detecting all pathogenic changes in a positive control set (N = 10). When applied to patients who previously had negative short-read testing (N = 39), additional diagnoses were uncovered in 13% of cases, including a novel methylation profile specific to spinal muscular atrophy, thus opening new avenues for diagnosing and treating this life-threatening condition. Our study illustrates the utility of LRS in clinical genetic testing and in the discovery of novel disease variations.