Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer

Zuojian Tang, Jared P. Steranka, Sisi Ma, Mark Grivainis, Nemanja Rodić, Cheng Ran Lisa Huang, Ie Ming Shih, Tian Li Wang, Jef D. Boeke, David Fenyö, Kathleen H. Burns

    Research output: Contribution to journalArticle

    Abstract

    Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq). We also report the development of a machine-learning-based computational pipeline, TIPseqHunter, to identify insertion sites with high precision and reliability. We demonstrate the utility of this approach to detect somatic retrotransposition events in highgrade ovarian serous carcinoma.

    Original languageEnglish (US)
    Pages (from-to)E733-E740
    JournalProceedings of the National Academy of Sciences of the United States of America
    Volume114
    Issue number5
    DOIs
    StatePublished - Jan 31 2017

    Keywords

    • Human
    • LINE-1
    • Ovarian cancer
    • Retrotransposon
    • TIPseq

    ASJC Scopus subject areas

    • General

    Fingerprint Dive into the research topics of 'Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer'. Together they form a unique fingerprint.

    Cite this