A cost-effective screen for identifying novel transposable element insertions in human genomes. E. M. Kvikstad, G. Lunter Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
Transposable elements (TEs) are mobile genetic elements that randomly insert copies of themselves into their hosts genome. As such, they are major drivers of genome evolution and responsible for substantial genomic variation between individuals. The potential mutational target for disease-causing TE insertions is large, as mutagenesis can occur by disrupting genes or modifying their expression through interference with proper splicing, disruption of exons, premature transcript termination or donating alternative transcription start sites. Since existing screens for mutations underlying disease typically ignore TE insertions, we hypothesize that the role of TEs in disease has thus far been underestimated.
Here, we present a cost-effective high-throughput and genome-wide screen for TE insertions to enable investigating the impact of TEs on disease. Briefly, the strategy consists of standard Illumina library preparation, followed by polymerase chain reaction (PCR) to enrich for genomic fragments containing sequence signatures of known active TEs subfamilies. Unlike existing approaches, our strategy simultaneously targets three of the most active and prolific TE subfamilies (AluYb8/b9, AluYa5, and human-specific L1HS elements) that together constitute only ~0.36% of the human genome, but the majority of polymorphic insertions. Preliminary results indicate that our approach yields up to 20,000-fold enrichment for targeted sequence fragments, each containing on average 62 nucleotides of unique sequence flanking the poly-A signature, allowing accurate mapping and detection of polymorphic and novel insertion sites.
Our protocol is compatible with exome sequencing protocols, and is particularly cost-effective in that setting by sharing the library preparation stage as well as allowing high levels of multiplexing. Therefore, applications of this protocol in parallel to whole-exome screens of sporadic disease cases will result in improved estimates of the contribution of TEs to sporadic disease, and potentially reduce the number of unresolved cases in such screens.
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