title: Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics.
abstract: BACKGROUND
  The revolution in cancer genomics shows that the dominant mutations are CG->TA transitions. The sources of these mutations are probably two host cell cytidine deaminases APOBEC3A and APOBEC3B. The former in particular can access nuclear DNA and monotonously introduce phenomenal numbers of C->T mutations in the signature 5'TpC context. These can be copied as G->A transitions in the 5'GpA context.
  
  
  METHODS
  DNA hypermutated by an APOBEC3 enzyme can be recovered by a technique called 3DPCR, which stands for differential DNA denaturation PCR. This method exploits the fact that APOBEC3-edited DNA is richer in A+T compared with the reference. We explore explicitly 3DPCR error using cloned DNA.
  
  
  RESULTS
  Here we show that the technique has a higher error rate compared with standard PCR and can generate DNA strands containing both C->T and G->A mutations in a 5'GpCpR context. Sequences with similar traits have been recovered from human tumour DNA using 3DPCR.
  
  
  CONCLUSIONS
  Differential DNA denaturation PCR cannot be used to identify fixed C->T transitions in cancer genomes. Presently, the overall mutation frequency is ∼10(4)-10(5) base substitutions per cancer genome, or 0.003-0.03 kb(-1). By contrast, the 3DPCR error rate is of the order of 4-20 kb(-1) owing to constant selection for AT DNA and PCR-mediated recombination. Accordingly, sequences recovered by 3DPCR harbouring mixed C->T and G->A mutations associated with the 5'GpC represent artefacts.
authors.affiliation: Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France.
authors.forename: R
authors.initials: R
authors.lastname: Suspène
authors.affiliation: Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France.
authors.forename: V
authors.initials: V
authors.lastname: Caval
authors.affiliation: Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France.
authors.forename: M
authors.initials: M
authors.lastname: Henry
authors.affiliation: Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France.
authors.forename: M S
authors.initials: MS
authors.lastname: Bouzidi
authors.affiliation: Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France.
authors.forename: S
authors.initials: S
authors.lastname: Wain-Hobson
authors.affiliation: Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France.
authors.forename: J-P
authors.initials: JP
authors.lastname: Vartanian
mesh_terms: D000071478:APOBEC Deaminases; D015496:CD4-Positive T-Lymphocytes / Q000187:drug effects / Q000378:metabolism; D006528:Carcinoma, Hepatocellular / Q000209:etiology / Q000235:genetics / Q000378:metabolism; D002478:Cells, Cultured; D003562:Cytidine / Q000378:metabolism; D003564:Cytidine Deaminase; D043525:Cytosine Deaminase / Q000378:metabolism*; D004273:DNA, Neoplasm / Q000235:genetics / Q000378:metabolism*; D019694:Hepatitis B, Chronic / Q000150:complications; D019698:Hepatitis C, Chronic / Q000150:complications; D006801:Humans; D016898:Interferon-alpha / Q000494:pharmacology; D007376:Interleukin-2 / Q000494:pharmacology; D008113:Liver Neoplasms / Q000209:etiology / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D009363:Neoplasm Proteins / Q000378:metabolism*; D009691:Nucleic Acid Denaturation; D010835:Phytohemagglutinins / Q000494:pharmacology; D016133:Polymerase Chain Reaction / Q000379:methods*; D011995:Recombination, Genetic; D013696:Temperature; D051176:beta Catenin / Q000235:genetics
chemical_list: C495270:CTNNB1 protein, human; D004273:DNA, Neoplasm; D016898:Interferon-alpha; D007376:Interleukin-2; D009363:Neoplasm Proteins; D010835:Phytohemagglutinins; D051176:beta Catenin; D003562:Cytidine; D043525:Cytosine Deaminase; D000071478:APOBEC Deaminases; C502889:APOBEC3 proteins, human; D003564:Cytidine Deaminase