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However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36 699 non-reference MEIs constructed from 5675 genomes, comprising 2998 Chinese samples (\u223c26.2\u00d7, NyuWa) and 2677 samples from the 1000 Genomes Project (\u223c7.4\u00d7, 1KGP). We discovered that LINE-1 insertions were highly enriched in centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.<\/jats:p>","DOI":"10.1093\/nar\/gkac128","type":"journal-article","created":{"date-parts":[[2022,2,11]],"date-time":"2022-02-11T15:10:18Z","timestamp":1644592218000},"page":"2493-2508","source":"Crossref","is-referenced-by-count":44,"title":["Characterizing mobile element insertions in 5675 genomes"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9694-8159","authenticated-orcid":false,"given":"Yiwei","family":"Niu","sequence":"first","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7258-3477","authenticated-orcid":false,"given":"Xueyi","family":"Teng","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Honghong","family":"Zhou","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yirong","family":"Shi","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanyan","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9484-3353","authenticated-orcid":false,"given":"Yiheng","family":"Tang","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9303-1639","authenticated-orcid":false,"given":"Peng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaxia","family":"Luo","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Kang","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"},{"name":"National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\u00a0100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7294-0865","authenticated-orcid":false,"given":"Shunmin","family":"He","sequence":"additional","affiliation":[{"name":"Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"},{"name":"College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,2,25]]},"reference":[{"key":"2022032100071114500_B1","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/S0959-437X(99)00031-3","article-title":"Interspersed repeats and other mementos of transposable elements in mammalian genomes","volume":"9","author":"Smit","year":"1999","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2022032100071114500_B2","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1016\/j.gde.2003.10.013","article-title":"Mobile elements and mammalian genome evolution","volume":"13","author":"Deininger","year":"2003","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2022032100071114500_B3","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1038\/nrg2640","article-title":"The impact of retrotransposons on human genome evolution","volume":"10","author":"Cordaux","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2022032100071114500_B4","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"2022032100071114500_B5","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s13100-016-0070-z","article-title":"Restricting retrotransposons: a review","volume":"7","author":"Goodier","year":"2016","journal-title":"Mobile DNA"},{"key":"2022032100071114500_B6","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.tig.2007.02.006","article-title":"Which transposable elements are active in the human genome","volume":"23","author":"Mills","year":"2007","journal-title":"Trends Genet."},{"key":"2022032100071114500_B7","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1146\/annurev-genet-110711-155616","article-title":"Active transposition in genomes","volume":"46","author":"Huang","year":"2012","journal-title":"Ann. rev. Genet."},{"key":"2022032100071114500_B8","doi-asserted-by":"crossref","first-page":"E2326","DOI":"10.1073\/pnas.1602336113","article-title":"Discovery of unfixed endogenous retrovirus insertions in diverse human populations","volume":"113","author":"Wildschutte","year":"2016","journal-title":"Proc. Nat. Acad. Sci. U.S.A."},{"key":"2022032100071114500_B9","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1038\/s41576-019-0165-8","article-title":"Transposable elements in human genetic disease","volume":"20","author":"Payer","year":"2019","journal-title":"Nat. Rev. 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Evol."},{"key":"2022032100071114500_B18","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/s41586-020-2287-8","article-title":"A structural variation reference for medical and population genetics","volume":"581","author":"Collins","year":"2020","journal-title":"Nature"},{"key":"2022032100071114500_B19","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/s41586-020-2371-0","article-title":"Mapping and characterization of structural variation in 17,795 human genomes","volume":"583","author":"Abel","year":"2020","journal-title":"Nature"},{"key":"2022032100071114500_B20","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.cell.2020.05.024","article-title":"Population structure, stratification, and introgression of human structural variation","volume":"182","author":"Almarri","year":"2020","journal-title":"Cell"},{"key":"2022032100071114500_B21","doi-asserted-by":"crossref","DOI":"10.2139\/ssrn.3967671","article-title":"High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios","author":"Byrska-Bishop","year":"2021"},{"key":"2022032100071114500_B22","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13100-015-0052-6","article-title":"Transposable element polymorphisms recapitulate human evolution","volume":"6","author":"Rishishwar","year":"2015","journal-title":"Mobile DNA"},{"key":"2022032100071114500_B23","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1016\/j.ajhg.2009.10.015","article-title":"Genomic dissection of population substructure of Han Chinese and its implication in association studies","volume":"85","author":"Xu","year":"2009","journal-title":"Am. 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Genet."},{"key":"2022032100071114500_B24","doi-asserted-by":"crossref","first-page":"110017","DOI":"10.1016\/j.celrep.2021.110017","article-title":"NyuWa Genome resource: a deep whole-genome sequencing-based variation profile and reference panel for the Chinese population","volume":"37","author":"Zhang","year":"2021","journal-title":"Cell Rep."},{"key":"2022032100071114500_B25","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"1000 Genomes Project Consortium","year":"2015","journal-title":"Nature"},{"key":"2022032100071114500_B26","article-title":"Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes","author":"Lowy-Gallego","year":"2018"},{"key":"2022032100071114500_B27","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2022032100071114500_B28","article-title":"Scaling accurate genetic variant discovery to tens of thousands of samples","author":"Poplin","year":"2018"},{"key":"2022032100071114500_B29","doi-asserted-by":"crossref","first-page":"2037","DOI":"10.1093\/bioinformatics\/btx100","article-title":"BCFtools\/csq: haplotype-aware variant consequences","volume":"33","author":"Danecek","year":"2017","journal-title":"Bioinformatics"},{"key":"2022032100071114500_B30","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nrg2165-c1","article-title":"A universal classification of eukaryotic transposable elements implemented in Repbase","volume":"9","author":"Kapitonov","year":"2008","journal-title":"Nat. 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Softw."},{"key":"2022032100071114500_B34","doi-asserted-by":"crossref","first-page":"D936","DOI":"10.1093\/nar\/gks1213","article-title":"DbVar and DGVa: public archives for genomic structural variation","volume":"41","author":"Lappalainen","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2022032100071114500_B35","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2022032100071114500_B36","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"2022032100071114500_B37","doi-asserted-by":"crossref","first-page":"D754","DOI":"10.1093\/nar\/gkx1098","article-title":"Ensembl 2018","volume":"46","author":"Zerbino","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022032100071114500_B38","doi-asserted-by":"crossref","first-page":"bax028","DOI":"10.1093\/database\/bax028","article-title":"GeneHancer: genome-wide integration of enhancers and target genes in GeneCards","volume":"2017","author":"Fishilevich","year":"2017","journal-title":"Database"},{"key":"2022032100071114500_B39","doi-asserted-by":"crossref","first-page":"E3984","DOI":"10.1073\/pnas.1704117114","article-title":"Structural variants caused by Alu insertions are associated with risks for many human diseases","volume":"114","author":"Payer","year":"2017","journal-title":"Proc. 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