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Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study

Journal of Human Genetics volume 65, pages 21–24 (2020)Cite this article

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Abstract

Short tandem repeats (STRs) are repetitive DNA sequences that are highly polymorphic and widely used for personal identification in the field of forensic medicine. The standard method for determining the repeat number of STRs is capillary electrophoresis of PCR products; however, the use of DNA sequencing has increased because it can identify same-sized alleles with nucleotide substitutions (iso-alleles). In this study, we performed human STR genotyping using a portable nanopore-based DNA sequencer, the MinION, and evaluated its performance. Because the sequence quality obtained by MinION is considerably lower than those obtained with other DNA sequencers, we developed an original scoring scheme for judging the genotypes from MinION reads. Analysis of seven human samples for 21–45 STR loci yielded an average of 857 thousand reads per sample, and the accuracy of genotyping and iso-allele identification reached 75.7% and 82%, respectively. Although the accuracy is higher than that reported previously, further improvements are required before this method can be practically applied.

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Acknowledgements

We thank Hisako Kawata of the Support Center for Medical Research and Education of Tokai University for providing excellent technical support. We also thank Drs. Douglas Storts and Spencer Hermanson of Promega Corp. for providing the PowerSeqTM System prototype.

Funding

This research was supported in part by joint-research funds from Tokai University provided by NEC Corporation.

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Authors and Affiliations

  1. 2nd Government and Public Solutions Division, NEC Corporation, Shiba 5-7-1, Minato-ku, Tokyo, 108-8001, Japan

    Minoru Asogawa & Masatoshi Sugisawa

  2. Biomedical Informatics Laboratory, Department of Molecular Life Science, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa, 259-1193, Japan

    Minoru Asogawa, Ayumu Ohno, So Nakagawa, Yasuhiro Katahira, Megumi Sudo & Tadashi Imanishi

  3. Micro/Nano Technology Center, Tokai University, Kitakaname 411, Hiratsuka, Kanagawa, 259-1292, Japan

    So Nakagawa

  4. Department of Forensic Medicine, Tokai University School of Medicine, Shimokasuya 143, Isehara, Kanagawa, 259-1193, Japan

    Eriko Ochiai & Motoki Osawa

  5. Genome Diversity Research Center, Tokai University Graduate School of Medicine, Shimokasuya 143, Isehara, Kanagawa, 259-1193, Japan

    Tadashi Imanishi

Authors
  1. Minoru Asogawa
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  2. Ayumu Ohno
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  3. So Nakagawa
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  4. Eriko Ochiai
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  5. Yasuhiro Katahira
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  6. Megumi Sudo
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  7. Motoki Osawa
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  8. Masatoshi Sugisawa
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  9. Tadashi Imanishi
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Correspondence to Minoru Asogawa or Tadashi Imanishi.

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This study was a joint-research project of NEC Corporation and Tokai University, which was financially supported by NEC Corporation.

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Asogawa, M., Ohno, A., Nakagawa, S. et al. Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study. J Hum Genet 65, 21–24 (2020). https://doi.org/10.1038/s10038-019-0688-z

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  • DOI: https://doi.org/10.1038/s10038-019-0688-z

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