Modeling the integration of bacterial rRNA fragments into the human cancer genome

Background Cancer is a disease driven by the accumulation of genomic alterations, including the integration of exogenous DNA into the human somatic genome. We previously identified in silico evidence of DNA fragments from a Pseudomonas-like bacteria integrating into the 5′-UTR of four proto-oncogenes in stomach cancer sequencing data. The functional and biological consequences of these bacterial DNA integrations remain unknown. Results Modeling of these integrations suggests that the previously identified sequences cover most of the sequence flanking the junction between the bacterial and human DNA. Further examination of these reads reveals that these integrations are rich in guanine nucleotides and the integrated bacterial DNA may have complex transcript secondary structures. Conclusions The models presented here lay the foundation for future experiments to test if bacterial DNA integrations alter the transcription of the human genes. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0982-0) contains supplementary material, which is available to authorized users.