@article {1611159, title = {Comprehensive identification of transposable element insertions using multiple sequencing technologies}, journal = {Nat Commun}, volume = {12}, number = {1}, year = {2021}, month = {2021 06 22}, pages = {3836}, abstract = {Transposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea .}, keywords = {DNA Transposable Elements, Gene Rearrangement, Genetic Variation, Genome, Human, Genomics, Haplotypes, Humans, Molecular Sequence Annotation, Mutagenesis, Insertional, Pseudogenes, Whole Genome Sequencing}, issn = {2041-1723}, doi = {10.1038/s41467-021-24041-8}, author = {Chu, Chong and Borges-Monroy, Rebeca and Viswanadham, Vinayak V and Lee, Soohyun and Li, Heng and Lee, Eunjung Alice** and Park, Peter J**} }