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

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 high-grade ovarian serous carcinoma.

SUBMITTER: Tang Z 

PROVIDER: S-EPMC5293032 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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

Tang Zuojian Z   Steranka Jared P JP   Ma Sisi S   Grivainis Mark M   Rodić Nemanja N   Huang Cheng Ran Lisa CR   Shih Ie-Ming IM   Wang Tian-Li TL   Boeke Jef D JD   Fenyö David D   Burns Kathleen H KH  

Proceedings of the National Academy of Sciences of the United States of America 20170117 5

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 selecti  ...[more]

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