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© Marie-Christine Prévost, Nathalie Sol-Foulon, Olivier Schwartz, Jean-Marc Panaud
AIDS virus particles at the surface of a lymphocyte.
Publication : British journal of cancer

Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in British journal of cancer - 01 Apr 2014

Suspène R, Caval V, Henry M, Bouzidi MS, Wain-Hobson S, Vartanian JP

Link to Pubmed [PMID] – 24691422

Br. J. Cancer 2014 May;110(10):2615-22

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.

http://www.ncbi.nlm.nih.gov/pubmed/24691422