title: Modeling the integration of bacterial rRNA fragments into the human cancer genome.
abstract: 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.
authors.affiliation: Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
authors.forename: Karsten B
authors.initials: KB
authors.lastname: Sieber
authors.affiliation: Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.|Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
authors.forename: Pawel
authors.initials: P
authors.lastname: Gajer
authors.affiliation: Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. jdhotopp@som.umaryland.edu.|Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. jdhotopp@som.umaryland.edu.|Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. jdhotopp@som.umaryland.edu.
authors.forename: Julie C
authors.initials: JC
authors.lastname: Dunning Hotopp
mesh_terms: D020121:5' Untranslated Regions; D015703:Antigens, CD / Q000235:genetics; D000944:Antigens, Differentiation, B-Lymphocyte / Q000235:genetics; D002272:Carcinoembryonic Antigen / Q000235:genetics; D015815:Cell Adhesion Molecules / Q000235:genetics; D058851:GPI-Linked Proteins / Q000235:genetics; D015894:Genome, Human; D000949:Histocompatibility Antigens Class II / Q000235:genetics; D006790:Host-Parasite Interactions / Q000235:genetics; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D009690:Nucleic Acid Conformation; D011549:Pseudomonas / Q000235:genetics*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011995:Recombination, Genetic
chemical_list: D020121:5' Untranslated Regions; D015703:Antigens, CD; D000944:Antigens, Differentiation, B-Lymphocyte; C527875:CEACAM5 protein, human; C504117:CEACAM6 protein, human; D002272:Carcinoembryonic Antigen; D015815:Cell Adhesion Molecules; D058851:GPI-Linked Proteins; D000949:Histocompatibility Antigens Class II; D012335:RNA, Ribosomal; C045084:invariant chain
keywords: Cancer genomics; DNA integration; Genome variation; Host-bacteria interactions; Somatic genome