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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Mobile elements create structural variation: Analysis of a complete human genome
Genome Research, Volume 19, No. 9, Year 2009
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Description
Structural variants (SVs) are common in the human genome. Because approximately half of the human genome consists of repetitive, transposable DNA sequences, it is plausible that these elements play an important role in generating SVs in humans. Sequencing of the diploid genome of one individual human (HuRef) affords us the opportunity to assess, for the first time, the impact of mobile elements on SVs in an individual in a thorough and unbiased fashion. In this study, we systematically evaluated more than 8000 SVs to identify mobile element-associated SVs as small as 100 bp and specific to the HuRef genome. Combining computational and experimental analyses, we identified and validated 706 mobile element insertion events (including Alu, L1, SVA elements, and nonclassical insertions), which added more than 305 kb of new DNA sequence to the HuRef genome compared with the Human Genome Project (HGP) reference sequence (hg18). We also identified 140 mobile element-associated deletions, which removed ∼126 kb of sequence from the HuRef genome. Overall, ∼10% of the HuRef-specific indels larger than 100 bp are caused by mobile element-associated events. More than one-third of the insertion/deletion events occurred in genic regions, and new Alu insertions occurred in exons of three human genes. Based on the number of insertions and the estimated time to the most recent common ancestor of HuRef and the HGP reference genome, we estimated the Alu, L1, and SVA retrotransposition rates to be one in 21 births, 212 births, and 916 births, respectively. This study presents the first comprehensive analysis of mobile element-related structural variants in the complete DNA sequence of an individual and demonstrates that mobile elements play an important role in generating inter-individual structural variation. © 2009 by Cold Spring Harbor Laboratory Press.
Authors & Co-Authors
Xing, Jinchuan
United States, Salt Lake City
University of Utah Health
Zhang, Yuhua
United States, Salt Lake City
University of Utah Health
Han, Kyudong
United States, Baton Rouge
Louisiana State University
Salem, Abdel Halim
United States, Baton Rouge
Louisiana State University
Egypt, Ismailia
Faculty of Medicine
Bahrain, Manama
Arabian Gulf University
Sen, Shurjo K.
United States, Baton Rouge
Louisiana State University
United States, Bethesda
National Human Genome Research Institute Nhgri
Huff, Chad D.
United States, Salt Lake City
University of Utah Health
Zhou, Qiong
United States, Salt Lake City
University of Utah Health
Kirkness, Ewen F.
United States, Rockville
J. Craig Venter Institute
Levy, Samuel
United States, Rockville
J. Craig Venter Institute
Batzer, Mark A.
United States, Baton Rouge
Louisiana State University
Jorde, Lynn B.
United States, Salt Lake City
University of Utah Health
Statistics
Citations: 296
Authors: 11
Affiliations: 6
Identifiers
Doi:
10.1101/gr.091827.109
ISSN:
10889051
e-ISSN:
15495469
Research Areas
Cancer
Genetics And Genomics