Mitochondrial DNA pseudogenes in the nuclear genome as possible sources of contamination

Abstract

The discovery in the nuclear DNA of sequences homologous to mitochondrial DNA raises the possibility that accidental amplifications may occur when performing PCR analyses. This issue gains importance in forensics where mtDNA is commonly used for identification purposes. We analysed 19 NUMTs that encompass the D-loop, and verified that it is unlikely that the primers usually used in forensics for HVR amplification accidentally anneal to the NUMT sequences. We also performed PCR analysis with primers specifically designed for mtDNA and NUMT sequences with 97% homology to the coding region. No accidental amplification of the NUMT occurred. Moreover, the NUMT sequences only amplified with the highest annealing temperatures of the NUMT specific primers. We conclude that the high number of mtDNA molecules in the tissues allows its amplification to be ensured, even when the primers also anneal in NUMT sequences.