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Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element

Jui Wan Loh1, Hongseok Ha1,2, Timothy Lin1

  • 11Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ 08854 USA.

Mobile DNA
|February 29, 2020
PubMed
Summary
This summary is machine-generated.

A new integrated Mobile Element Scanning (ME-Scan) protocol efficiently identifies polymorphic mobile element insertions (pMEIs) from three active human retrotransposon families. This cost-effective method offers high accuracy for genomic variation studies.

Keywords:
AluYbHigh-throughput sequencingLINE-1ME-ScanMobile element insertionRetrotransposonSVA

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Mobile elements comprise over half of the human genome and are key drivers of genomic variation.
  • Polymorphic mobile element insertions (pMEIs) influence gene expression, genome stability, and disease susceptibility.

Purpose of the Study:

  • To develop an integrated Mobile Element Scanning (ME-Scan) protocol for identifying multiple active human mobile element families.
  • To establish a cost-effective and flexible method for detecting polymorphic mobile element insertions (pMEIs).

Main Methods:

  • Developed an integrated ME-Scan protocol to selectively amplify insertion sites of active retrotransposons (AluYb, L1HS, SVA).
  • Utilized pooled library preparation for simultaneous sequencing of multiple mobile element families.
  • Applied the protocol to 12 human parent-offspring trios and analyzed data with a dedicated computational pipeline.

Main Results:

  • Achieved high sensitivity (>90%) and accuracy (>95%) in identifying pMEIs across three major mobile element families.
  • Demonstrated the protocol's capability to detect somatic insertions.
  • Successfully identified pMEIs from AluYb, L1HS, and SVA families in a single sequencing run.

Conclusions:

  • The integrated ME-Scan protocol provides a cost-effective and efficient approach for novel pMEI discovery in the human genome.
  • The protocol's flexibility allows adaptation for detecting various mobile element families and potential application in other species.
  • A complete framework, including library design, sequencing, and analysis pipeline, is provided for widespread researcher adoption.