Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection
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Wei Zhang | Liqin Xu | Bo Li | Xiaosen Guo | Nannan Li | Qichao Yu | Guibo Li | Wei Zhang | Xiaosen Guo | Shiping Liu | Yongli Zeng | Guibo Li | Qichao Yu | Yanhui Wang | Liqin Xu | Shiping Liu | Xiaolong Zhang | Yongli Zeng | Yeming Wang | Yanhui Wang | Xiaoyun Huang | Xinlan Zhou | Jie Lu | Yong Hou | Xiaolong Zhang | Yeming Wang | Xiaoyun Huang | Nannan Li | Xinlan Zhou | Jie Lu | Yong Hou | Bo Li
[1] Richard Cordaux,et al. Estimating the retrotransposition rate of human Alu elements. , 2006, Gene.
[2] H. Harn,et al. Angiotensin I converting enzyme gene polymorphism in Chinese patients with hypertension. , 1997, American journal of hypertension.
[3] F. Tajima. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.
[4] T. Kurtz,et al. Frequency of a deletion polymorphism in the gene for angiotensin converting enzyme is increased in African-Americans with hypertension. , 1994, American journal of hypertension.
[5] Nansheng Chen,et al. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.
[6] Lovelace J. Luquette,et al. Landscape of Somatic Retrotransposition in Human Cancers , 2012, Science.
[7] S. Boissinot,et al. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. , 2000, Molecular biology and evolution.
[8] X. Xie,et al. Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell , 2012, Science.
[9] Sébastien Tempel. Using and understanding RepeatMasker. , 2012, Methods in molecular biology.
[10] Dawei Li,et al. The diploid genome sequence of an Asian individual , 2008, Nature.
[11] E. Kirkness,et al. Mobile elements create structural variation: analysis of a complete human genome. , 2009, Genome research.
[12] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[13] B. Morris,et al. Association of a polymorphism of the angiotensin I-converting enzyme gene with essential hypertension. , 1992, Biochemical and biophysical research communications.
[14] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[15] Faraz Hach,et al. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery , 2010, Bioinform..
[16] R. J. Herrera,et al. African origin of human-specific polymorphic Alu insertions. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[17] M. Batzer,et al. Alu repeats and human genomic diversity , 2002, Nature Reviews Genetics.
[18] D. Largaespada,et al. Extensive somatic L1 retrotransposition in colorectal tumors , 2012, Genome research.
[19] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[20] A. Troxel,et al. Genomic characterization of recent human LINE-1 insertions: evidence supporting random insertion. , 2001, Genome research.
[21] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[22] E. Eichler,et al. A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms , 2010, Cell.
[23] Ryan D. Hernandez,et al. Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome , 2008, PLoS genetics.
[24] Piero Carninci,et al. Edinburgh Research Explorer Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma , 2022 .
[25] M. Batzer,et al. The impact of retrotransposons on human genome evolution , 2009, Nature Reviews Genetics.
[26] P Corvol,et al. An insertion/deletion polymorphism in the angiotensin I-converting enzyme gene accounting for half the variance of serum enzyme levels. , 1990, The Journal of clinical investigation.
[27] Thomas M. Keane,et al. Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly , 2010, Genome Biology.
[28] J. V. Moran,et al. Hot L1s account for the bulk of retrotransposition in the human population , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[29] J. Mattick,et al. Somatic retrotransposition alters the genetic landscape of the human brain , 2011, Nature.
[30] G. Swergold,et al. Tracing the LINEs of human evolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[31] D. C. Hancks,et al. Active human retrotransposons: variation and disease. , 2012, Current opinion in genetics & development.
[32] A. F. Scott,et al. Isolation of an active human transposable element. , 1991, Science.
[33] Maite G. Barrón,et al. T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data , 2014, bioRxiv.
[34] L. Jorde,et al. Mobile element biology: new possibilities with high-throughput sequencing. , 2013, Trends in genetics : TIG.
[35] Deepak Grover,et al. dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans , 2006, Human mutation.
[36] Deniz Yorukoglu,et al. Alu repeat discovery and characterization within human genomes. , 2011, Genome research.
[37] International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome , 2001, Nature.
[38] S. Yusuf,et al. Differences in risk factors, atherosclerosis, and cardiovascular disease between ethnic groups in Canada: the Study of Health Assessment and Risk in Ethnic groups (SHARE) , 2000, The Lancet.
[39] A. Asamoah,et al. A deletion in the angiotensin converting enzyme (ACE) gene is common among African Americans with essential hypertension , 1996 .
[40] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[41] Gabor T. Marth,et al. An integrated map of structural variation in 2,504 human genomes , 2015, Nature.
[42] X. Huang,et al. CAP3: A DNA sequence assembly program. , 1999, Genome research.
[43] Thomas M. Keane,et al. RetroSeq: transposable element discovery from next-generation sequencing data , 2013, Bioinform..
[44] Adrian M. Stütz,et al. A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans , 2011, PLoS genetics.
[45] H. Kazazian,et al. Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. , 2011, Genome research.
[46] Kai Ye,et al. Mobster: accurate detection of mobile element insertions in next generation sequencing data , 2014, Genome Biology.
[47] Huanming Yang,et al. Deep whole-genome sequencing of 90 Han Chinese genomes , 2017, GigaScience.
[48] J. Boeke,et al. Human Transposon Tectonics , 2012, Cell.
[49] Qichao Yu. Simulating reads for detection of transportable element insertions , 2018 .
[50] Zhen Yue,et al. pIRS: Profile-based Illumina pair-end reads simulator , 2012, Bioinform..