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Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics

R Suspène 1 V Caval 1 M Henry 1 M Bouzidi 1 S Wain-Hobson 1 Jean Pierre Vartanian 1, * 
* Corresponding author
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.
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Submitted on : Monday, January 10, 2022 - 6:42:00 PM
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R Suspène, V Caval, M Henry, M Bouzidi, S Wain-Hobson, et al.. Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics. British Journal of Cancer, Cancer Research UK, 2014, 110 (10), pp.2615-2622. ⟨10.1038/bjc.2014.176⟩. ⟨pasteur-03520069⟩

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