Characterizing mobile element insertions in 5675 genomes
Abstract Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to t...
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| Veröffentlicht in: | Nucleic acids research 2022-03, Vol.50 (5), p.2493-2508 |
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| creator | Niu, Yiwei Teng, Xueyi Zhou, Honghong Shi, Yirong Li, Yanyan Tang, Yiheng Zhang, Peng Luo, Huaxia Kang, Quan Xu, Tao He, Shunmin |
| description | Abstract
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. 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 (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 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. |
| doi_str_mv | 10.1093/nar/gkac128 |
| format | Article |
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Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. 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 (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 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.</description><identifier>ISSN: 0305-1048</identifier><identifier>ISSN: 1362-4962</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkac128</identifier><identifier>PMID: 35212372</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Data Resources and Analyses ; Genome, Human ; Humans ; Long Interspersed Nucleotide Elements - genetics ; Polymorphism, Single Nucleotide</subject><ispartof>Nucleic acids research, 2022-03, Vol.50 (5), p.2493-2508</ispartof><rights>The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. 2022</rights><rights>The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c478t-15055fe3a7d6256fe9edf06239dab037786ee64171570f7fffd35eda013bdb153</citedby><cites>FETCH-LOGICAL-c478t-15055fe3a7d6256fe9edf06239dab037786ee64171570f7fffd35eda013bdb153</cites><orcidid>0000-0002-7294-0865 ; 0000-0002-9694-8159 ; 0000-0001-9303-1639 ; 0000-0002-9484-3353 ; 0000-0001-7258-3477</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8934628/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8934628/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35212372$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Niu, Yiwei</creatorcontrib><creatorcontrib>Teng, Xueyi</creatorcontrib><creatorcontrib>Zhou, Honghong</creatorcontrib><creatorcontrib>Shi, Yirong</creatorcontrib><creatorcontrib>Li, Yanyan</creatorcontrib><creatorcontrib>Tang, Yiheng</creatorcontrib><creatorcontrib>Zhang, Peng</creatorcontrib><creatorcontrib>Luo, Huaxia</creatorcontrib><creatorcontrib>Kang, Quan</creatorcontrib><creatorcontrib>Xu, Tao</creatorcontrib><creatorcontrib>He, Shunmin</creatorcontrib><title>Characterizing mobile element insertions in 5675 genomes</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. 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 (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 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.</description><subject>Data Resources and Analyses</subject><subject>Genome, Human</subject><subject>Humans</subject><subject>Long Interspersed Nucleotide Elements - genetics</subject><subject>Polymorphism, Single Nucleotide</subject><issn>0305-1048</issn><issn>1362-4962</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kE1LxDAQhoMo7rp68i49iSB189Ek7UWQxS9Y8KLnkLaT3WibrEkr6K-3uuuiF08zMA_vOzwIHRN8QXDBpk6H6eJFV4TmO2hMmKBpVgi6i8aYYZ4SnOUjdBDjM8YkIzzbRyPGKaFM0jHKZ0sddNVBsB_WLZLWl7aBBBpowXWJdRFCZ72Lw5pwIXmyAOdbiIdoz-gmwtFmTtDTzfXj7C6dP9zez67maZXJvEsJx5wbYFrWgnJhoIDaYEFZUesSMylzASAyIgmX2EhjTM041BoTVtYl4WyCLte5q75soa6Gr4Ju1CrYVod35bVVfy_OLtXCv6m8YJmg-RBwtgkI_rWH2KnWxgqaRjvwfVRUMJYLLr-7ztdoFXyMAcy2hmD15VoNrtXG9UCf_P5sy_7IHYDTNeD71b9Jn7WTiNA</recordid><startdate>20220321</startdate><enddate>20220321</enddate><creator>Niu, Yiwei</creator><creator>Teng, Xueyi</creator><creator>Zhou, Honghong</creator><creator>Shi, Yirong</creator><creator>Li, Yanyan</creator><creator>Tang, Yiheng</creator><creator>Zhang, Peng</creator><creator>Luo, Huaxia</creator><creator>Kang, Quan</creator><creator>Xu, Tao</creator><creator>He, Shunmin</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-7294-0865</orcidid><orcidid>https://orcid.org/0000-0002-9694-8159</orcidid><orcidid>https://orcid.org/0000-0001-9303-1639</orcidid><orcidid>https://orcid.org/0000-0002-9484-3353</orcidid><orcidid>https://orcid.org/0000-0001-7258-3477</orcidid></search><sort><creationdate>20220321</creationdate><title>Characterizing mobile element insertions in 5675 genomes</title><author>Niu, Yiwei ; Teng, Xueyi ; Zhou, Honghong ; Shi, Yirong ; Li, Yanyan ; Tang, Yiheng ; Zhang, Peng ; Luo, Huaxia ; Kang, Quan ; Xu, Tao ; He, Shunmin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c478t-15055fe3a7d6256fe9edf06239dab037786ee64171570f7fffd35eda013bdb153</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Data Resources and Analyses</topic><topic>Genome, Human</topic><topic>Humans</topic><topic>Long Interspersed Nucleotide Elements - genetics</topic><topic>Polymorphism, Single Nucleotide</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Niu, Yiwei</creatorcontrib><creatorcontrib>Teng, Xueyi</creatorcontrib><creatorcontrib>Zhou, Honghong</creatorcontrib><creatorcontrib>Shi, Yirong</creatorcontrib><creatorcontrib>Li, Yanyan</creatorcontrib><creatorcontrib>Tang, Yiheng</creatorcontrib><creatorcontrib>Zhang, Peng</creatorcontrib><creatorcontrib>Luo, Huaxia</creatorcontrib><creatorcontrib>Kang, Quan</creatorcontrib><creatorcontrib>Xu, Tao</creatorcontrib><creatorcontrib>He, Shunmin</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Niu, Yiwei</au><au>Teng, Xueyi</au><au>Zhou, Honghong</au><au>Shi, Yirong</au><au>Li, Yanyan</au><au>Tang, Yiheng</au><au>Zhang, Peng</au><au>Luo, Huaxia</au><au>Kang, Quan</au><au>Xu, Tao</au><au>He, Shunmin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterizing mobile element insertions in 5675 genomes</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2022-03-21</date><risdate>2022</risdate><volume>50</volume><issue>5</issue><spage>2493</spage><epage>2508</epage><pages>2493-2508</pages><issn>0305-1048</issn><issn>1362-4962</issn><eissn>1362-4962</eissn><abstract>Abstract
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. 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 (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>35212372</pmid><doi>10.1093/nar/gkac128</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0002-7294-0865</orcidid><orcidid>https://orcid.org/0000-0002-9694-8159</orcidid><orcidid>https://orcid.org/0000-0001-9303-1639</orcidid><orcidid>https://orcid.org/0000-0002-9484-3353</orcidid><orcidid>https://orcid.org/0000-0001-7258-3477</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Data Resources and Analyses Genome, Human Humans Long Interspersed Nucleotide Elements - genetics Polymorphism, Single Nucleotide |
| title | Characterizing mobile element insertions in 5675 genomes |
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