@article {152866, title = {Landscape of somatic retrotransposition in human cancers.}, journal = {Science}, volume = {337}, number = {6097}, year = {2012}, month = {2012 Aug 24}, pages = {967-71}, abstract = { Transposable elements (TEs) are abundant in the human genome, and some are capable of generating new insertions through RNA intermediates. In cancer, the disruption of cellular mechanisms that normally suppress TE activity may facilitate mutagenic retrotranspositions. We performed single-nucleotide resolution analysis of TE insertions in 43 high-coverage whole-genome sequencing data sets from five cancer types. We identified 194 high-confidence somatic TE insertions, as well as thousands of polymorphic TE insertions in matched normal genomes. Somatic insertions were present in epithelial tumors but not in blood or brain cancers. Somatic L1 insertions tend to occur in genes that are commonly mutated in cancer, disrupt the expression of the target genes, and are biased toward regions of cancer-specific DNA hypomethylation, highlighting their potential impact in tumorigenesis. }, keywords = {Base Sequence, Cell Transformation, Neoplastic, Colorectal Neoplasms, DNA Methylation, Female, Gene Expression Regulation, Neoplastic, Genes, Neoplasm, Genome, Human, Glioblastoma, Humans, Long Interspersed Nucleotide Elements, Male, Microsatellite Instability, Molecular Sequence Annotation, Molecular Sequence Data, Multiple Myeloma, Mutagenesis, Insertional, Mutation, Ovarian Neoplasms, Prostatic Neoplasms, Retroelements, Sequence Analysis, DNA}, issn = {1095-9203}, doi = {10.1126/science.1222077}, author = {Lee, Eunjung and Iskow, Rebecca and Yang, Lixing and Gokcumen, Omer and Haseley, Psalm and Luquette, Lovelace J and Lohr, Jens G and Harris, Christopher C and Ding, Li and Wilson, Richard K and Wheeler, David A and Gibbs, Richard A and Kucherlapati, Raju and Lee, Charles and Kharchenko, Peter V** and Park, Peter J** and Cancer Genome Atlas Research Network, The Cancer Genome Atlas} }