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Long-read sequencing revealing intragenic deletions in exome-negative spastic paraplegias

Journal of Human Genetics volume 68, pages 689–697 (2023)Cite this article

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Abstract

Hereditary spastic paraplegias (HSPs) are a heterogeneous group of neurodegenerative disorders characterized by progressive spasticity and weakness in the lower extremities. To date, a total of 88 types of SPG are known. To diagnose HSP, multiple technologies, including microarray, direct sequencing, multiplex ligation-dependent probe amplification, and short-read next-generation sequencing, are often chosen based on the frequency of HSP subtypes. Exome sequencing (ES) is commonly used. We used ES to analyze ten cases of HSP from eight families. We identified pathogenic variants in three cases (from three different families); however, we were unable to determine the cause of the other seven cases using ES. We therefore applied long-read sequencing to the seven undetermined HSP cases (from five families). We detected intragenic deletions within the SPAST gene in four families, and a deletion within PSEN1 in the remaining family. The size of the deletion ranged from 4.7 to 12.5 kb and involved 1–7 exons. All deletions were entirely included in one long read. We retrospectively performed an ES-based copy number variation analysis focusing on pathogenic deletions, but were not able to accurately detect these deletions. This study demonstrated the efficiency of long-read sequencing in detecting intragenic pathogenic deletions in ES-negative HSP patients.

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Acknowledgements

We would like to thank all the subjects for participating in this study. We also thank N. Watanabe, T. Miyama, M. Sato, S. Sugimoto, and K. Takabe for technical assistance. We are grateful to Anahid Pinchis and Alison Inglis, PhD, from Edanz (https://jp.edanz.com/ac) for editing a draft of this manuscript. This work was supported by the Japan Agency for Medical Research and Development (AMED) under grant numbers JP22ek0109595h0001 (HD) and JP22ek0109486, JP22ek0109549, and JP22ek0109493 (NM); JSPS KAKENHI under grant numbers JP23H02829 (SM), JP21K15907 (YU), JP22K15646 (KH), JP21K07869 (EK), JP22K15901 (AF), JP21K07298 (HD), JP21K07440 (FT) and JP23H02877 (TM); the Takeda Science Foundation (HD, NM, and TM); Health Labour Sciences Research Grants from the Ministry of Health, Labour and Welfare (202011073A, 202011029A; FT) and a grant for Strategic Research Promotion from Yokohama City University (SK2804; FT).

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Authors and Affiliations

  1. Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan

    Hiromi Fukuda, Takeshi Mizuguchi, Shinichi Kameyama, Sachiko Ohori, Eriko Koshimizu, Yuri Uchiyama, Naomi Tsuchida, Atsushi Fujita, Kohei Hamanaka, Kazuharu Misawa, Satoko Miyatake & Naomichi Matsumoto

  2. Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan

    Hiromi Fukuda, Hiroshi Doi, Misako Kunii, Hideto Joki, Hiroyasu Komiya, Yosuke Miyaji & Fumiaki Tanaka

  3. Department of Pathology, Keio University School of Medicine, Tokyo, 160-8582, Japan

    Shinichi Kameyama

  4. Department of Neurology, National Hospital Organization Yokohama Medical Center, Yokohama, Kanagawa, 245-8575, Japan

    Hideto Joki & Tatsuya Takahashi

  5. Department of Neurology, Yokohama Minami Kyosai Hospital, Yokohama, 236-0037, Japan

    Mei Sasaki

  6. Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, 236-0004, Japan

    Sachiko Ohori & Satoko Miyatake

  7. Department of Genetics, Kitasato University Hospital, Sagamihara, 252-0375, Japan

    Sachiko Ohori

  8. Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, 236-0004, Japan

    Yuri Uchiyama & Naomi Tsuchida

  9. RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan

    Kazuharu Misawa

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  1. Hiromi Fukuda
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Contributions

HF and NM contributed to the study design. HF, HD, SK, SO, EK, YU, NT, AF, KH, KM, SM, TM and NM performed the data analysis. HD, MK, HJ, TT, HK, MS, YM and FT evaluated clinical information of patients. HF, TM and NM prepared the manuscript. NM finalized the manuscript. All authors critically reviewed and revised the manuscript and approved the final version for submission.

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Correspondence to Takeshi Mizuguchi or Naomichi Matsumoto.

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Fukuda, H., Mizuguchi, T., Doi, H. et al. Long-read sequencing revealing intragenic deletions in exome-negative spastic paraplegias. J Hum Genet 68, 689–697 (2023). https://doi.org/10.1038/s10038-023-01170-0

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