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

European Journal of Human Genetics (2025)Cite this article

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Abstract

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.

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Fig. 1: Representative brain magnetic resonance imaging (MRI), histopathological features, initial detection of GGC repeat expansion of the patient, and primer design schematic.
Fig. 2: Visualization of LRS data and genotyping of GGC repeat expansion in NOTCH2NLC.

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Data availability

The data supporting the findings of this study are available from the corresponding author upon reasonable request.

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Acknowledgements

We express our sincere gratitude to all participants for their invaluable collaboration, as well as to the patients’ families for their understanding and assistance.

Funding

This study was supported by the Science and Technology Program of Zhejiang Province (2024C03100), the Zhejiang Provincial Natural Science Foundation of China (LQ24H090009), the Medical Science and Technology Project of Zhejiang Province (2024KY539), the National Natural Science Foundation of China (82450114) and the Zhejiang Provincial Natural Science Foundation of China (LY23H090010).

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Author notes

  1. These authors contributed equally: Xiaosheng Zheng, Nan Jin.

Authors and Affiliations

  1. Department of Neurology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China

    Xiaosheng Zheng, Nan Jin, Dehao Yang, Lebo Wang, Yixin Kang, Zhidong Cen & Wei Luo

  2. Department of Neurology, Taizhou Central Hospital, Taizhou University Hospital, Taizhou, Zhejiang, China

    Peng Liu

  3. Department of General Practice and International Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China

    Jiaxiang Li

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  1. Xiaosheng Zheng
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  2. Nan Jin
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  3. Peng Liu
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  9. Wei Luo
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Contributions

Conceptualization and design: XZ, NJ, and WL; Methodology: XZ, NJ, and PL; Validation: DY and JL; Formal Analysis: NJ, DY, and LW; Investigation: XZ, NJ, and PL; Resources: XZ and NJ; Data Curation: DY, LW, YK, JL, and ZC; Writing – Original Draft Preparation: XZ, NJ, and PL; Writing – Review & Editing: XZ, NJ, PL, DY, LW, YK, JL, ZC, and WL; Visualization: PL and DY; Supervision: WL and XZ; Project Administration: WL and XZ; Funding Acquisition: WL.

Corresponding author

Correspondence to Wei Luo.

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All subjects provided written informed consent. The study received approval from the Ethics Committee of the Second Affiliated Hospital of Zhejiang University.

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Zheng, X., Jin, N., Liu, P. et al. Detection and characterization of rare variants in NOTCH2NLC causing false negative molecular diagnosis through long-read sequencing. Eur J Hum Genet (2025). https://doi.org/10.1038/s41431-025-01892-z

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  • DOI: https://doi.org/10.1038/s41431-025-01892-z

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