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Open Access Research article

The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation

Ryan L Parr1*, Jennifer Maki1, Brian Reguly1, Gabriel D Dakubo1, Andrea Aguirre1, Roy Wittock1, Kerry Robinson1, John P Jakupciak2 and Robert E Thayer1

Author Affiliations

1 Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada

2 Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA

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BMC Genomics 2006, 7:185  doi:10.1186/1471-2164-7-185

Published: 21 July 2006

Abstract

Background

Nuclear mitochondrial pseudogenes (numts) are a potential source of contamination during mitochondrial DNA PCR amplification. This possibility warrants careful experimental design and cautious interpretation of heteroplasmic results.

Results

Here we report the cloning and sequencing of numts loci, amplified from human tissue and rho-zero (ρ0) cells (control) with primers known to amplify the mitochondrial genome. This paper is the first to fully sequence 46 paralogous nuclear DNA fragments that represent the entire mitochondrial genome. This is a surprisingly small number due primarily to the primer sets used in this study, because prior to this, BLAST searches have suggested that nuclear DNA harbors between 400 to 1,500 paralogous mitochondrial DNA fragments. Our results indicate that multiple numts were amplified simultaneously with the mitochondrial genome and increased the load of pseudogene signal in PCR reactions. Further, the entire mitochondrial genome was represented by multiple copies of paralogous nuclear sequences.

Conclusion

These findings suggest that mitochondrial genome disease-associated biomarkers must be rigorously authenticated to preclude any affiliation with paralogous nuclear pseudogenes. Importantly, the common perception that mitochondrial template "swamps" numts loci precluding detectable amplification, depends on the region of the mitochondrial genome targeted by the PCR reaction and the number of pseudogene loci that may co-amplify. Cloning and relevant sequencing data will facilitate the correct interpretation. This is the first complete, wet-lab characterization of numts that represent the entire mitochondrial genome.