![]() ![]() Regarding the mechanism of insertion, non-LTR retrotransposition in mammals is driven by the activity of Long INterspersed Elements (LINEs) which replicate through an mRNA-mediated series of events known as target-primed reverse transcription (TPRT). This review is principally concerned with the detection of non-Long Terminal Repeat (LTR) retrotransposons in mammalian genomes, but many of the concepts should generalise to other transposable element types in other species. Transposable elements represent a majority of structural insertions longer than a few hundred base pairs, and require a further level of scrutiny on top of what is normally required for SV detection, which is informed by their insertion mechanism. ![]() The endpoints not corresponding to the insertion site map to TE elements at various locations in the reference genome Panel b shows a typical pattern of discordant read mappings across a genome - the colored segments in circle represent chromosomes, each black link indicates a discordant read mapping supporting an insertion at the position indicated by the red triangle. If a TSD is not present (and no bases are deleted upon insertion), the junctions obtained from the 5' end and the 3' end of the TE reference will match exactly. If a TSD is present, the insertion breakends relative to the reference genome are staggered, and the overlap of reference-aligned sequence corresponds to the TSD. Assembly of the reads supporting the two junction sequences is indicated to the right of the ‘consensus’ arrow, one example with a TSD and one without. The exact location of this example insertion is indicated by the red triangle and the dashed line. Within the informative reads, reads or portions of reads mapping to the TE reference are coloured blue, and mappings to the reference genome sequence are coloured yellow. Reads informative for identifying TE insertion locations are indicated by dashed boxes, other read mappings to the TE reference are shown in light blue boxes. Reads are represented as typical paired-end reads where the ends of each amplicon are represented as rectangles and the un-sequenced portion of the amplicons are represented as bars connecting the rectangles. Panel a shows the read mapping patterns versus a reference TE sequence (grey rectangle, top) and the mapping of the same reads to a reference genome sequence (orange rectangle, bottom). Read mapping patterns typically associated with insertion detection. sequence assembly and re-alignment of assembled contigs. clustering of ‘split’ reads sharing common alignment junctions, and 3. ![]() inference from discordant read-pair mappings, 2. Typically, structural variant detection from short paired-end read data is solved through a combination of three approaches: 1. Detection of structural variants is more difficult, principally because using current whole genome sequencing methods, the presence of rearrangements versus the reference genome must be inferred from short sequences that generally do not span the entire interval affected by a rearrangement. Detection of small mutations, single-base or multiple-base substitutions, insertions, and deletions less than one read length, is achievable through accurate alignment to the reference genome followed by examination of aligned columns of bases for deviations from the reference sequence. The majority of the WGS data available today comes from Illumina platforms and consists of millions to billions of 100-150 bp reads in pairs, where each read in a pair represents the end of a longer fragment (Fig. This review focuses on methods for discovering and/or genotyping transposable elements from whole genome sequence (WGS) data. Similarly, there are several methods used for transposable element identification and annotation from genome assemblies, also reviewed elsewhere. A number of targeted methods are available to sequence junctions between TEs and their insertion sites, and have been reviewed elsewhere. Identification of transposable element insertions (TEs) from the results of currently available high-throughput sequencing platforms is a challenge. Because LINEs, Alus, and SVAs are actively increasing in copy number at estimated rates of around 2-5 new insertions for every 100 live births for Alu, and around 0.5-1 in 100 for L1, it stands to reason that the vast majority of transposable element insertions are not present in the reference genome assembly and are detectable as segregating structural variants in human populations. published the seminal observation of active LINE-1 retrotransposition in humans, and 14 years since the initial publication of the assembled human genome reference sequence gave us a genome-wide view of human transposable element content, albeit largely from one individual. It has been 27 years since Haig Kazazian, Jr. ![]()
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