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Lee, Eunjung

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Eunjung

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Lee, Eunjung

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2012 - 20163

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Author's Publications: search.filters.isAuthorOfPublication.b0e7e36c-4517-484f-8fe2-cd14ed09b469

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Now showing 1 - 3 of 3
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    Next-generation sequencing-based detection of germline L1-mediated transductions
    (BioMed Central, 2016) Tica, Jelena; Lee, Eunjung; Untergasser, Andreas; Meiers, Sascha; Garfield, David A.; Gokcumen, Omer; Furlong, Eileen E.M.; Park, Peter; Stütz, Adrian M.; Korbel, Jan O.
    Background: While active LINE-1 (L1) elements possess the ability to mobilize flanking sequences to different genomic loci through a process termed transduction influencing genomic content and structure, an approach for detecting polymorphic germline non-reference transductions in massively-parallel sequencing data has been lacking. Results: Here we present the computational approach TIGER (Transduction Inference in GERmline genomes), enabling the discovery of non-reference L1-mediated transductions by combining L1 discovery with detection of unique insertion sequences and detailed characterization of insertion sites. We employed TIGER to characterize polymorphic transductions in fifteen genomes from non-human primate species (chimpanzee, orangutan and rhesus macaque), as well as in a human genome. We achieved high accuracy as confirmed by PCR and two single molecule DNA sequencing techniques, and uncovered differences in relative rates of transduction between primate species. Conclusions: By enabling detection of polymorphic transductions, TIGER makes this form of relevant structural variation amenable for population and personal genome analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2670-x) contains supplementary material, which is available to authorized users.
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    Resolving rates of mutation in the brain using single-neuron genomics
    (eLife Sciences Publications, Ltd, 2016) Evrony, Gilad D; Lee, Eunjung; Park, Peter; Walsh, Christopher
    Whether somatic mutations contribute functional diversity to brain cells is a long-standing question. Single-neuron genomics enables direct measurement of somatic mutation rates in human brain and promises to answer this question. A recent study (Upton et al., 2015) reported high rates of somatic LINE-1 element (L1) retrotransposition in the hippocampus and cerebral cortex that would have major implications for normal brain function, and suggested that these events preferentially impact genes important for neuronal function. We identify aspects of the single-cell sequencing approach, bioinformatic analysis, and validation methods that led to thousands of artifacts being interpreted as somatic mutation events. Our reanalysis supports a mutation frequency of approximately 0.2 events per cell, which is about fifty-fold lower than reported, confirming that L1 elements mobilize in some human neurons but indicating that L1 mosaicism is not ubiquitous. Through consideration of the challenges identified, we provide a foundation and framework for designing single-cell genomics studies. DOI: http://dx.doi.org/10.7554/eLife.12966.001
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    Analysis of somatic retrotransposition in human cancers
    (BioMed Central, 2012) Lee, Eunjung; Iskow, Rebecca; Yang, Lixing; Gokcumen, Omer; Haseley, Psalm; Luquette, Joe; Lohr, Jens; Harris, Christopher C; Ding, Li; Wilson, Richard K.; Wheeler, David A.; Gibbs, Richard A; Kucherlapati, Raju; Lee, Charles; Kharchenko, Peter; Park, Peter