Homo sapiens Raw sequence reads

Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These are self-propagating mobile DNAs, 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. We describe in detail a protocol for the selective amplification of Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. We also describe the development of a machine learning-based computational pipeline for transposon insertion profiling by sequencing (TIPseq). This pipeline, TIPseqHunter, is designed 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. We also introduce TranspoScope, an online tool for visualizing TIPseq data.