title: 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.
authors.affiliation: Center for Health Informatics and Bioinformatics, NYU Langone Medical Center, New York, NY 10016.|Institute for Systems Genetics, NYU Langone Medical Center, New York, NY 10016.
authors.forename: Zuojian
authors.initials: Z
authors.lastname: Tang
authors.affiliation: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205.|McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
authors.forename: Jared P
authors.initials: JP
authors.lastname: Steranka
authors.affiliation: Center for Health Informatics and Bioinformatics, NYU Langone Medical Center, New York, NY 10016.
authors.forename: Sisi
authors.initials: S
authors.lastname: Ma
authors.affiliation: Center for Health Informatics and Bioinformatics, NYU Langone Medical Center, New York, NY 10016.|Institute for Systems Genetics, NYU Langone Medical Center, New York, NY 10016.
authors.forename: Mark
authors.initials: M
authors.lastname: Grivainis
authors.affiliation: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
authors.forename: Nemanja
authors.initials: N
authors.lastname: Rodić
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
authors.forename: Cheng Ran Lisa
authors.initials: CR
authors.lastname: Huang
authors.affiliation: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205.|Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
authors.forename: Ie-Ming
authors.initials: IM
authors.lastname: Shih
authors.affiliation: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
authors.forename: Tian-Li
authors.initials: TL
authors.lastname: Wang
authors.affiliation: Institute for Systems Genetics, NYU Langone Medical Center, New York, NY 10016; jef.boeke@nyumc.org david@fenyolab.org kburns@jhmi.edu.
authors.forename: Jef D
authors.identifier: 0000-0001-5322-4946
authors.initials: JD
authors.lastname: Boeke
authors.affiliation: Center for Health Informatics and Bioinformatics, NYU Langone Medical Center, New York, NY 10016; jef.boeke@nyumc.org david@fenyolab.org kburns@jhmi.edu.|Institute for Systems Genetics, NYU Langone Medical Center, New York, NY 10016.
authors.forename: David
authors.initials: D
authors.lastname: Fenyö
authors.affiliation: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205; jef.boeke@nyumc.org david@fenyolab.org kburns@jhmi.edu.|McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205.
authors.forename: Kathleen H
authors.identifier: 0000-0003-1620-3761
authors.initials: KH
authors.lastname: Burns
mesh_terms: D000465:Algorithms; D005260:Female; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D000069550:Machine Learning; D010051:Ovarian Neoplasms / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods
keywords: LINE-1; TIPseq; human; ovarian cancer; retrotransposon