![]() ![]() ![]() 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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