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Elements and Compounds01:27

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Pure substances consist of only one type of matter. A pure substance can be an element or a compound. An element consists of only one type of atom, while a compound consists of two or more types of atoms held together by a chemical bond.
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A high throughput screen for active human transposable elements.

Erika M Kvikstad1,2, Paolo Piazza3,4, Jenny C Taylor3,5

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Summary
This summary is machine-generated.

Transposable elements (TEs) are mobile genetic sequences. A new method, TE-NGS, efficiently identifies novel and polymorphic TE insertions, aiding disease research.

Keywords:
AluBioinformaticsLINE1Next generation sequencingPolymorphismTransposable elements

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Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Transposable elements (TEs) are mobile genetic sequences that can affect gene transcription and cause disease.
  • Identifying TE insertions is challenging, hindering disease impact assessment.
  • Three TE subfamilies (L1HS, AluYa5/8, AluYb8/9) account for most recent TE activity.

Purpose of the Study:

  • To develop a targeted sequencing protocol and computational pipeline for identifying polymorphic and novel TE insertions.
  • To create a method that simultaneously targets major active TE subfamilies.
  • To reduce input material and experimental complexity for TE insertion analysis.

Main Methods:

  • Developed TE-NGS, a targeted sequencing protocol and computational pipeline.
  • Utilized next-generation sequencing for TE insertion identification.
  • Focused on L1HS, AluYa5/8, and AluYb8/9 subfamilies.

Main Results:

  • Demonstrated high sensitivity and precision for identifying TE insertions in NA12878.
  • Reported 17 previously unreported TE insertion loci in NA12878, validated by long-read evidence.
  • Identified 1470 polymorphic and novel TEs across 12 additional samples, previously undocumented.

Conclusions:

  • TE-NGS facilitates the identification of polymorphic and novel TE insertions.
  • Future applications of TE-NGS with exome sequencing may resolve more sporadic disease cases.
  • This method can improve understanding of TE contributions to human genetic disease.