Characterization of full-length LINE-1 insertions in 154 genomes |
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| Institution: | 1. School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America;2. Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, Philadelphia, PA, United States of America;1. Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA;2. National Center for Biodefense and Infectious Disease, Laboratory of Molecular Virology, George Mason University, Manassas, VA 20110, USA;1. Department of Human Anatomy and Histology-Embryology, School of Basic Medical Sciences, Xi''an Jiaotong University Health Science Center, Xi''an 710061, Shaanxi, China;2. Jinzhou Medical UniversiIty, Jinzhou 121000, China;3. Institute of Neuroscience, School of Basic Medical Sciences, Xi''an Jiaotong University Health Science Center, Xi''an 710061, Shaanxi, China;1. Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima str. 10, 10-748 Olsztyn, Poland;2. INRAE, UR1037 Fish Physiology and Genomics, F-35000 Rennes, France;3. Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany;4. Sigenae, UR875, INRAE, 31326 Castanet-Tolosan, France;5. Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Poland;6. Department of Salmonid Research, The Stanislaw Sakowicz Inland Fisheries Institute, Olsztyn, Poland;7. University of Lorraine, INRAE, UR AFPA, F-54000 Nancy, France;1. Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, China;2. School of Public Health, Southwest Medical University, Luzhou 646000, China;3. Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China;4. Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Southwest Medical University, Luzhou 646000, China |
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| Abstract: | Long interspersed nuclear elements (LINEs) are retrotransposons that contribute to genetic variation in the human genome. LINE-1 elements in larger-scale studies are challenging to identify using sequencing technologies due to cost and scalability. We developed an approach using optical mapping for detection of full-length LINE-1 insertions and 10× sequencing for confirmation. We found 51 true positive full-length LINE-1 insertions, of which 4 are novel insertions, in NA12878. Repeating our analysis on a larger sample set representing 26 populations, we identified 329 full-length LINE-1 elements, of which 123 are novel. 24.8% of these 329 LINE-1 insertions were shared amongst all 5 superpopulations (AFR, AMR, EUR, EAS, SAS). The African superpopulation has a higher percentage of population-specific LINE-1 insertions than any other superpopulation. These data indicate that our approach can provide high-speed, cost-effective, and increased accuracy for LINE-1 detection. These data also provide an insight into variations of LINE-1 elements between different populations. |
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