{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,11,22]],"date-time":"2023-11-22T03:52:17Z","timestamp":1700625137434},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"S9","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>In humans, copies of the Long Interspersed Nuclear Element 1 (LINE-1) retrotransposon comprise 21% of the reference genome, and have been shown to modulate expression and produce novel splice isoforms of transcripts from genes that span or neighbor the LINE-1 insertion site.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this work, newly released pilot data from the 1000 Genomes Project is analyzed to detect previously unreported full length insertions of the retrotransposon LINE-1. By direct analysis of the sequence data, we have identified 22 previously unreported LINE-1 insertion sites within the sequence data reported for a mother\/father\/daughter trio.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>It is demonstrated here that next generation sequencing data, as well as emerging high quality datasets from individual genome projects allow us to assess the amount of heterogeneity with respect to the LINE-1 retrotransposon amongst humans, and provide us with a wealth of testable hypotheses as to the impact that this diversity may have on the health of individuals and populations.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-s9-s12","type":"journal-article","created":{"date-parts":[[2010,10,28]],"date-time":"2010-10-28T18:15:23Z","timestamp":1288289723000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data"],"prefix":"10.1186","volume":"11","author":[{"given":"Eric","family":"Rouchka","sequence":"first","affiliation":[]},{"given":"Diego E","family":"Montoya-Durango","sequence":"additional","affiliation":[]},{"given":"Vilius","family":"Stribinskis","sequence":"additional","affiliation":[]},{"given":"Kenneth","family":"Ramos","sequence":"additional","affiliation":[]},{"given":"Ted","family":"Kalbfleisch","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,10,28]]},"reference":[{"issue":"6822","key":"4274_CR1","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/35057062","volume":"409","author":"ES Lander","year":"2001","unstructured":"Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al.: Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860\u2013921. 10.1038\/35057062","journal-title":"Nature"},{"issue":"9","key":"4274_CR2","doi-asserted-by":"publisher","first-page":"5280","DOI":"10.1073\/pnas.0831042100","volume":"100","author":"B Brouha","year":"2003","unstructured":"Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, Kazazian HH Jr.: Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 2003, 100(9):5280\u20135285. 10.1073\/pnas.0831042100","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"4274_CR3","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1016\/j.gde.2003.10.013","volume":"13","author":"PL Deininger","year":"2003","unstructured":"Deininger PL, Moran JV, Batzer MA, Kazazian HH Jr.: Mobile elements and mammalian genome evolution. Curr Opin Genet Dev 2003, 13(6):651\u2013658. 10.1016\/j.gde.2003.10.013","journal-title":"Curr Opin Genet Dev"},{"issue":"6","key":"4274_CR4","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1002\/humu.20486","volume":"28","author":"DV Babushok","year":"2007","unstructured":"Babushok DV, Kazazian HH Jr.: Progress in understanding the biology of the human mutagen LINE-1. Hum Mutat 2007, 28(6):527\u2013539. 10.1002\/humu.20486","journal-title":"Hum Mutat"},{"issue":"2","key":"4274_CR5","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1534\/genetics.104.031757","volume":"168","author":"EA Bennett","year":"2004","unstructured":"Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE: Natural genetic variation caused by transposable elements in humans. Genetics 2004, 168(2):933\u2013951. 10.1534\/genetics.104.031757","journal-title":"Genetics"},{"issue":"1-2","key":"4274_CR6","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.gene.2006.07.040","volume":"390","author":"MK Konkel","year":"2007","unstructured":"Konkel MK, Wang J, Liang P, Batzer MA: Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. Gene 2007, 390(1\u20132):28\u201338. 10.1016\/j.gene.2006.07.040","journal-title":"Gene"},{"issue":"6","key":"4274_CR7","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1101\/gr.075770.107","volume":"18","author":"K Akagi","year":"2008","unstructured":"Akagi K, Li J, Stephens RM, Volfovsky N, Symer DE: Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res 2008, 18(6):869\u2013880. 10.1101\/gr.075770.107","journal-title":"Genome Res"},{"issue":"1","key":"4274_CR8","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/ng0598-19","volume":"19","author":"HH Kazazian Jr.","year":"1998","unstructured":"Kazazian HH Jr., Moran JV: The impact of L1 retrotransposons on the human genome. Nat Genet 1998, 19(1):19\u201324. 10.1038\/ng0598-19","journal-title":"Nat Genet"},{"issue":"8","key":"4274_CR9","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1002\/bies.20257","volume":"27","author":"JS Han","year":"2005","unstructured":"Han JS, Boeke JD: LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression? Bioessays 2005, 27(8):775\u2013784. 10.1002\/bies.20257","journal-title":"Bioessays"},{"issue":"12","key":"4274_CR10","first-page":"6718","volume":"10","author":"GD Swergold","year":"1990","unstructured":"Swergold GD: Identification, characterization, and cell specificity of a human LINE-1 promoter. Mol Cell Biol 1990, 10(12):6718\u20136729.","journal-title":"Mol Cell Biol"},{"issue":"6","key":"4274_CR11","doi-asserted-by":"publisher","first-page":"1973","DOI":"10.1128\/MCB.21.6.1973-1985.2001","volume":"21","author":"M Speek","year":"2001","unstructured":"Speek M: Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Cell Biol 2001, 21(6):1973\u20131985. 10.1128\/MCB.21.6.1973-1985.2001","journal-title":"Mol Cell Biol"},{"issue":"5","key":"4274_CR12","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1006\/geno.2002.6758","volume":"79","author":"P Nigumann","year":"2002","unstructured":"Nigumann P, Redik K, Matlik K, Speek M: Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics 2002, 79(5):628\u2013634. 10.1006\/geno.2002.6758","journal-title":"Genomics"},{"issue":"10","key":"4274_CR13","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1111\/j.1365-2443.2007.01117.x","volume":"12","author":"I Teneng","year":"2007","unstructured":"Teneng I, Stribinskis V, Ramos KS: Context-specific regulation of LINE-1. Genes Cells 2007, 12(10):1101\u20131110. 10.1111\/j.1365-2443.2007.01117.x","journal-title":"Genes Cells"},{"issue":"5","key":"4274_CR14","doi-asserted-by":"publisher","first-page":"2616","DOI":"10.1158\/0008-5472.CAN-05-3478","volume":"66","author":"V Stribinskis","year":"2006","unstructured":"Stribinskis V, Ramos KS: Activation of human long interspersed nuclear element 1 retrotransposition by benzo(a)pyrene, an ubiquitous environmental carcinogen. Cancer Res 2006, 66(5):2616\u20132620. 10.1158\/0008-5472.CAN-05-3478","journal-title":"Cancer Res"},{"issue":"30","key":"4274_CR15","doi-asserted-by":"publisher","first-page":"28201","DOI":"10.1074\/jbc.M303888200","volume":"278","author":"KP Lu","year":"2003","unstructured":"Lu KP, Ramos KS: Redox regulation of a novel L1Md-A2 retrotransposon in vascular smooth muscle cells. J Biol Chem 2003, 278(30):28201\u201328209. 10.1074\/jbc.M303888200","journal-title":"J Biol Chem"},{"issue":"3","key":"4274_CR16","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403\u2013410.","journal-title":"J Mol Biol"},{"issue":"17","key":"4274_CR17","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"4274_CR18","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ: BLAT--the BLAST-like alignment tool. Genome Res 2002, 12(4):656\u2013664.","journal-title":"Genome Res"},{"issue":"10","key":"4274_CR19","doi-asserted-by":"publisher","first-page":"e254","DOI":"10.1371\/journal.pbio.0050254","volume":"5","author":"S Levy","year":"2007","unstructured":"Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, et al.: The diploid genome sequence of an individual human. PLoS Biol 2007, 5(10):e254. 10.1371\/journal.pbio.0050254","journal-title":"PLoS Biol"},{"issue":"7189","key":"4274_CR20","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1038\/nature06884","volume":"452","author":"DA Wheeler","year":"2008","unstructured":"Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, et al.: The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452(7189):872\u2013876. 10.1038\/nature06884","journal-title":"Nature"},{"issue":"9","key":"4274_CR21","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1038\/nbt.1561","volume":"27","author":"D Pushkarev","year":"2009","unstructured":"Pushkarev D, Neff NF, Quake SR: Single-molecule sequencing of an individual human genome. Nat Biotechnol 2009, 27(9):847\u2013852. 10.1038\/nbt.1561","journal-title":"Nat Biotechnol"},{"key":"4274_CR22","volume-title":"In: In Sequence. GenomeWeb News","author":"J Karow","year":"2009","unstructured":"Karow J: Complete Genomics Delivers 14 Human Genomes; Pfizer Among Customers. In: In Sequence. GenomeWeb News 2009."},{"issue":"1","key":"4274_CR23","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1101\/gr.4001406","volume":"16","author":"H Khan","year":"2006","unstructured":"Khan H, Smit A, Boissinot S: Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 2006, 16(1):78\u201387. 10.1101\/gr.4001406","journal-title":"Genome Res"},{"issue":"6","key":"4274_CR24","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1093\/oxfordjournals.molbev.a026372","volume":"17","author":"S Boissinot","year":"2000","unstructured":"Boissinot S, Chevret P, Furano AV: L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol 2000, 17(6):915\u2013928.","journal-title":"Mol Biol Evol"},{"issue":"2","key":"4274_CR25","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/S0378-1119(96)00856-6","volume":"189","author":"K Hata","year":"1997","unstructured":"Hata K, Sakaki Y: Identification of critical CpG sites for repression of L1 transcription by DNA methylation. Gene 1997, 189(2):227\u2013234. 10.1016\/S0378-1119(96)00856-6","journal-title":"Gene"},{"issue":"1-2","key":"4274_CR26","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.mrfmmm.2009.02.011","volume":"665","author":"DE Montoya-Durango","year":"2009","unstructured":"Montoya-Durango DE, Liu Y, Teneng I, Kalbfleisch T, Lacy ME, Steffen MC, Ramos KS: Epigenetic control of mammalian LINE-1 retrotransposon by retinoblastoma proteins. Mutat Res 2009, 665(1\u20132):20\u201328.","journal-title":"Mutat Res"},{"issue":"6160","key":"4274_CR27","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1038\/332164a0","volume":"332","author":"HH Kazazian Jr.","year":"1988","unstructured":"Kazazian HH Jr., Wong C, Youssoufian H, Scott AF, Phillips DG, Antonarakis SE: Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature 1988, 332(6160):164\u2013166. 10.1038\/332164a0","journal-title":"Nature"},{"key":"4274_CR28","unstructured":"NCBI hosted ftp site for pilot data produced in by the 1000 genomes project[ftp:\/\/ftp-trace.ncbi.nih.gov\/1000genomes\/ftp\/pilot_data\/data]"},{"key":"4274_CR29","first-page":"365","volume":"132","author":"S Rozen","year":"2000","unstructured":"Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132: 365\u2013386.","journal-title":"Methods Mol Biol"},{"key":"4274_CR30","doi-asserted-by":"publisher","first-page":"1262","DOI":"10.1101\/gr.106419.110","volume":"20","author":"AD Ewing","year":"2010","unstructured":"Ewing AD, Kazazian HH Jr.: High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 2010, 20: 1262\u20131270. 10.1101\/gr.106419.110","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-S9-S12.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T04:38:06Z","timestamp":1630471086000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-S9-S12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10]]},"references-count":30,"journal-issue":{"issue":"S9","published-print":{"date-parts":[[2010,10]]}},"alternative-id":["4274"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-s9-s12","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,10]]},"assertion":[{"value":"28 October 2010","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S12"}}