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Gigascience. 2017 Sep 1;6(9):1-11. doi: 10.1093/gigascience/gix066.

Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection.

Yu Q1,2, Zhang W1,2, Zhang X2, Zeng Y2, Wang Y2, Wang Y2, Xu L2, Huang X2, Li N2, Zhou X2, Lu J3, Guo X2, Li G2,4, Hou Y2,4, Liu S2,5, Li B2,6.

Author information

BGI Education Center, UCAS: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
BGI College: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
Department of Biology, University of Copenhagen: Nørregade 10, Copenhagen 1165, Denmark.
School of Biology and Biological Engineering, SCUT: Postdoctoral Apartment Building, South China University of Technology, Wushan RD., TianHe District, Guangzhou, 510640, China.
BGI-Forensics: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.


Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high-depth whole-genome sequencing data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population of 90 Han Chinese individuals with a mean ×68 depth per individual. In total, we identify 9342 recent RIPs, and 8433 of these RIPs are novel compared with dbRIP, including 5826 Alu, 2169 long interspersed nuclear element 1 (L1), 383 SVA, and 55 long terminal repeats. Among the 9342 RIPs, 4828 were located in gene regions and 5 were located in protein-coding regions. We demonstrate that RIPs can, in principle, be an informative resource to perform population evolution and phylogenetic analyses. Taking the demographic effects into account, we identify a weak negative selection on SVA and L1 but an approximately neutral selection for Alu elements based on the frequency spectrum of RIPs. SID is a powerful open-source program for the detection of non-reference RIPs. We built a non-reference RIP dataset that greatly enhanced the diversity of RIPs detected in the general population, and it should be invaluable to researchers interested in many aspects of human evolution, genetics, and disease. As a proof of concept, we demonstrate that the RIPs can be used as biomarkers in a similar way as single nucleotide polymorphisms.


next-generation sequencing; retrotransposon insertion polymorphism; transposable element; whole-genome sequencing

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