Landscape of somatic retrotransposition in human cancers

Eunjung Lee, Rebecca Iskow, Lixing Yang, Omer Gokcumen, Psalm Haseley, Lovelace J. Luquette, Jens G. Lohr, Christopher C. Harris, Li Ding, Richard K. Wilson, David A. Wheeler, Richard A. Gibbs, Raju Kucherlapati, Charles Lee, Peter V. Kharchenko, Peter J. Park

Research output: Contribution to journalArticlepeer-review

522 Scopus citations


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.

Original languageEnglish
Pages (from-to)967-971
Number of pages5
Issue number6097
StatePublished - Aug 24 2012


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