NanoRanger enables rapid single base-pair resolution of genomic disorders

Rare diseases affect around 350 million individuals globally, yet at least half of those with suspected Mendelian disorders remain without a precise molecular diagnosis despite advanced genetic testing using short read sequencing (SRS). Long-read sequencing (LRS) holds a promise in addressing this diagnostic gap although its clinical application is hampered by its complicated workflow, demanding sample requirements, and exorbitant cost. Genomic disorders represent an opportunity to demonstrate the unique capability of LRS. This study addresses the challenges of identifying missing disease-causing breakpoints in complex genomic disorders by employing multiple LRS strategies, including a novel strategy named nanopore-based rapid acquisition of neighboring genomic regions (NanoRanger). NanoRanger requires neither detailed prior genetic mapping nor large amounts of ultrahigh-molecular-weight DNA, and it stands out for its ease of use and ultra-rapid acquisition of large genomic regions of interest with deep coverage. We describe a cohort of 13 families, each harboring a different homozygous disease-causing genomic rearrangement that defied breakpoint determination by SRS and Optical Genome Mapping (OGM). In each case, NanoRanger identified the breakpoints with a single base-pair resolution. This has enabled the accurate determination of the carrier status of unaffected family members as well as the founder nature of these genomic lesions and their frequency in the local population. It has also enabled an unprecedented analysis of the DNA motifs to discern the mechanism that predisposed to these recessive rearrangements. Our data suggest that NanoRanger can greatly accelerate the clinical adoption of LRS and expand its access for the benefit of patients with rare diseases.