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Significance Much of our genome is repetitive sequence. This property poses challenges for investigators because differences in repetitive sequences are difficult to detect. With hundreds of thousands of similar repeats, it has been difficult to discern how one person’s genome differs from another person’s genome or how tumor DNA differs from normal DNA. To solve this issue, we developed methods to target next-generation sequencing to the insertion sites of the most variable repeats. Computational pipelines to make these studies scalable and more widely accessible were needed, however. Here, we report a pipeline that accomplishes this goal. We use it to demonstrate insertions of the long interspersed element-1 (LINE-1) acquired in ovarian cancer that may contribute to the development of these tumors.

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