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Application of targeted nanopore sequencing for the screening and determination of structural variants in patients with Lynch syndrome

Journal of Human Genetics volume 66, pages 1053–1060 (2021)Cite this article

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Abstract

Lynch syndrome is a hereditary disease characterized by an increased risk of colorectal and other cancers. Germline variants in the mismatch repair (MMR) genes are responsible for this disease. Previously, we screened the MMR genes in colorectal cancer patients who fulfilled modified Amsterdam II criteria, and multiplex ligation-dependent probe amplification (MPLA) identified 11 structural variants (SVs) of MLH1 and MSH2 in 17 patients. In this study, we have tested the efficacy of long read-sequencing coupled with target enrichment for the determination of SVs and their breakpoints. DNA was captured by array probes designed to hybridize with target regions including four MMR genes and then sequenced using MinION, a nanopore sequencing platform. Approximately, 1000-fold coverage was obtained in the target regions compared with other regions. Application of this system to four test cases among the 17 patients correctly mapped the breakpoints. In addition, we newly found a deletion across an 84 kb region of MSH2 in a case without the pathogenic single nucleotide variants. These data suggest that long read-sequencing combined with hybridization-based enrichment is an efficient method to identify both SVs and their breakpoints. This strategy might replace MLPA for the screening of SVs in hereditary diseases.

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Acknowledgements

The super-computing resource was provided by Human Genome Center, Institute of Medical Science, The University of Tokyo (http://sc.hgc.jp/shirokane.html).

Fundings

This work was supported in part by the Grant-in-Aid #16H01569 (Y.F.) from the Japan Society for the Promotion of Science, and Center of Innovation program (S.M. and S.I.) from the Japan Science and Technology Agency.

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Author notes

  1. These authors contributed equally: Kiyoshi Yamaguchi, Rika Kasajima

Authors and Affiliations

  1. Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan

    Kiyoshi Yamaguchi, Kiyoko Takane, Seira Hatakeyama, Yoichi Furukawa & Tsuneo Ikenoue

  2. Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan

    Rika Kasajima, Eigo Shimizu, Rui Yamaguchi, Kotoe Katayama, Satoru Miyano & Seiya Imoto

  3. Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Kanagawa, 241-8518, Japan

    Rika Kasajima

  4. Division of Cancer Systems Biology, Aichi Cancer Center Research Institute, Aichi, 464-8681, Japan

    Rui Yamaguchi

  5. Division of Cancer Informatics, Nagoya University Graduate School of Medicine, Aichi, 466-8550, Japan

    Rui Yamaguchi

  6. The Committee of HNPCC Registry and Genetic Testing Project, Japanese Society for Cancer of the Colon and Rectum (JSCCR), Tokyo, 102-0075, Japan

    Masami Arai, Chikashi Ishioka, Takeo Iwama, Satoshi Kaneko, Nagahide Matsubara, Yoshihiro Moriya, Tadashi Nomizu, Kokichi Sugano, Kazuo Tamura, Naohiro Tomita, Teruhiko Yoshida, Kenichi Sugihara & Yoichi Furukawa

  7. Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan

    Yusuke Nakamura

  8. Systems Biology for Intractable Diseases, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan

    Satoru Miyano

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  1. Kiyoshi Yamaguchi
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Correspondence to Yoichi Furukawa.

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Yamaguchi, K., Kasajima, R., Takane, K. et al. Application of targeted nanopore sequencing for the screening and determination of structural variants in patients with Lynch syndrome. J Hum Genet 66, 1053–1060 (2021). https://doi.org/10.1038/s10038-021-00927-9

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  • DOI: https://doi.org/10.1038/s10038-021-00927-9

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