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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Mobile elements create structural variation: analysis of a complete human genome.

Jinchuan Xing1, Yuhua Zhang, Kyudong Han

  • 1Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84109, USA.

Genome Research
|May 15, 2009
PubMed
Summary
This summary is machine-generated.

Mobile elements like Alu and L1 significantly contribute to structural variants (SVs) in the human genome. This study reveals their role in generating new DNA insertions and deletions, impacting human genetic diversity.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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Area of Science:

  • Genomics
  • Molecular Biology
  • Human Genetics

Background:

  • Structural variants (SVs) are prevalent in the human genome.
  • Repetitive and transposable DNA sequences constitute a substantial portion of the human genome.
  • Mobile elements are hypothesized to be key drivers of SV formation.

Purpose of the Study:

  • To comprehensively analyze the impact of mobile elements on structural variants in an individual human genome (HuRef).
  • To identify and quantify mobile element-associated insertions and deletions.
  • To estimate retrotransposition rates for major mobile element families.

Main Methods:

  • Systematic evaluation of over 8000 structural variants in the HuRef genome.
  • Integration of computational and experimental analyses to identify mobile element-associated SVs.
  • Comparison with the Human Genome Project (HGP) reference sequence (hg18).

Main Results:

  • Identified 706 mobile element insertion events (Alu, L1, SVA) adding over 305 kb of DNA.
  • Detected 140 mobile element-associated deletions removing approximately 126 kb of sequence.
  • Approximately 10% of HuRef-specific indels (>100 bp) are mobile element-associated; over a third occur in genic regions.

Conclusions:

  • Mobile elements are a significant source of structural variation between individuals.
  • New mobile element insertions, including Alu insertions in gene exons, can alter human gene function.
  • Estimated Alu, L1, and SVA retrotransposition rates provide insights into ongoing genome evolution.