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

SUBMITTER: Suspene R 

PROVIDER: S-EPMC4021520 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature