Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data

Eric Rouchka, Diego E. Montoya-Durango, Vilius Stribinskis, Kenneth Ramos, Ted Kalbfleisch

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: In humans, copies of the Long Interspersed Nuclear Element 1 (LINE-1) retrotransposon comprise 21% of the reference genome, and have been shown to modulate expression and produce novel splice isoforms of transcripts from genes that span or neighbor the LINE-1 insertion site.Results: In this work, newly released pilot data from the 1000 Genomes Project is analyzed to detect previously unreported full length insertions of the retrotransposon LINE-1. By direct analysis of the sequence data, we have identified 22 previously unreported LINE-1 insertion sites within the sequence data reported for a mother/father/daughter trio.Conclusions: It is demonstrated here that next generation sequencing data, as well as emerging high quality datasets from individual genome projects allow us to assess the amount of heterogeneity with respect to the LINE-1 retrotransposon amongst humans, and provide us with a wealth of testable hypotheses as to the impact that this diversity may have on the health of individuals and populations.

Original languageEnglish (US)
Article numberS12
JournalBMC Bioinformatics
Volume11
Issue numberSUPPL. 9
DOIs
StatePublished - Oct 28 2010
Externally publishedYes

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Genetic Variation
Retroelements
Genes
Genome
Insertion
Nuclear Family
Fathers
Sequence Analysis
Protein Isoforms
Mothers
Sequencing
Health
Population
Gene

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. / Rouchka, Eric; Montoya-Durango, Diego E.; Stribinskis, Vilius; Ramos, Kenneth; Kalbfleisch, Ted.

In: BMC Bioinformatics, Vol. 11, No. SUPPL. 9, S12, 28.10.2010.

Research output: Contribution to journalArticle

Rouchka, Eric ; Montoya-Durango, Diego E. ; Stribinskis, Vilius ; Ramos, Kenneth ; Kalbfleisch, Ted. / Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. In: BMC Bioinformatics. 2010 ; Vol. 11, No. SUPPL. 9.
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