Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method

  • Shin, Wonseok (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University) ;
  • Mun, Seyoung (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University) ;
  • Kim, Junse (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University) ;
  • Lee, Wooseok (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University) ;
  • Park, Dong-Guk (Department of Surgery, Dankook University College of Medicine) ;
  • Choi, Seungkyu (Department of Pathology, Dankook University College of Medicine) ;
  • Lee, Tae Yoon (Department of Technology Education and Department of Biomedical Engineering, Chungnam National University) ;
  • Cha, Seunghee (Department of Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry) ;
  • Han, Kyudong (Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University)
  • Received : 2018.08.17
  • Accepted : 2018.10.26
  • Published : 2019.01.31


Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.

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Fig. 1. The workflow of L1Hs-targeted enrichment library preparation.

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Fig. 2. The design of the probe specific for the L1Hs-target sequence.

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Fig. 3. NGS Data analysis.

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Fig. 4. Comparison of the L1 composition on the genes of non-reference L1Hs insertion and on the human genes.

Table 1. Summary of the high-throughput sequencing data

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Table 2. Summary of non-reference L1Hs elements in the KPGP9 genome

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Supported by : National Research Foundation of Korea (NRF)


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