期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 114, 期 5, 页码 E733-E740出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1619797114
关键词
retrotransposon; TIPseq; human; LINE-1; ovarian cancer
资金
- Sol Goldman Pancreatic Cancer Research Center
- Health, Empowerment, Research, and Awareness Women's Cancer Foundation
- Burroughs Wellcome Fund Career Award for Biomedical Scientists Program
- US NIH Awards [R01CA161210, R01CA163705, R01GM103999]
- National Institute of General Medical Sciences Center for Systems Biology of Retrotransposition Grant [P50GM107632]
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.
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