Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data.
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.
Computer Engineering and Computer Science Department, Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA. eric.rouchka@louisville.edu
Eric
E
Rouchka
Diego E
DE
Montoya-Durango
Vilius
V
Stribinskis
Kenneth
K
Ramos
Ted
T
Kalbfleisch
D001483:Base Sequence; D030541:Databases, Genetic; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny