Detection and characterization of rare variants in NOTCH2NLC causing false negative molecular diagnosis through long-read sequencing.

Neuronal intranuclear inclusion disease (NIID) is typically diagnosed through molecular techniques or skin biopsy, with GGC repeat expansions in NOTCH2NLC being a key molecular marker. This study investigated an NIID patient who had received skin biopsy confirmation but showed no detectable GGC repeat expansions in NOTCH2NLC through standard genetic testing. Using whole genome long-read sequencing (LRS), we identified GGC expansions in NOTCH2NLC along with three previously undetected upstream variants that had caused the initial false-negative molecular diagnosis. We further analyzed 501 essential tremor patients and 361 whole genome LRS datasets to characterize the region surrounding the GGC repeat expansion, revealing that these variants are rare. Our findings demonstrate that rare NOTCH2NLC variants can lead to false-negative molecular diagnoses in NIID patients, emphasizing the value of comprehensive genotyping through LRS. These results provide important guidance for developing diagnostic strategies for similar cases in the future.