TransgeneR: a one-stop tool for transgene integration and rearrangement discovery using sequencing data

Abstract

Genetically modified organisms are widely used in lifescience research, agriculture and in commercial products. However, in most cases, the genetic modification in the host genome is often less well characterized with respect to integration location, copy number and host gene expression. The application of next generation sequencing technologies has enabled the characterization of transgene events but still limited by the lack of computational tools. We present a one-stop R tool, transgeneR, as a general computational tool for discovering transgene integration and rearrangement in the host genome. It especially considers the properties of transgene events, such as the homologous transgene sequences, complex genetic structure and multiple copies of transgene insertion. Using this tool, we have successfully mapped the chromosomal transgene integration loci and transgene rearrangements in an artificially simulated MAPT transgene mice genome as well as in a newly generated human tau (MAPT, 0N4R) transgene mice. When unbiased sequencing data such as the whole genome sequencing data, were provided as input, transgeneR integrated multiple information, including integration location, direction, split- and nonsplit-reads, to predict the transgene fragments and their copy number. Overall, our initial evaluation indicates that the transgeneR package is an effective tool for the identification and characterization of transgene integration and rearrangements events, especially in transgene genome with complex genetic structure. TransgeneR is publicly available: https://github.com/menggf/transgeneR