The Pseudo-mitochondrial Genome Influences Mistakes in Heteroplasmy Interpretation

Published

July 21, 2006

Author(s)

Ryan L. Parr, Jennifer Maki, Brian Reguly, Gabriel D. Dakubo, A A. Aguirre, Roy Wittock, Kerry Robinson, J P. Jakupciak, Robert E. Thayer

Abstract

Nuclear mitochondrial pseudogenes (numts) are a potential source of contamination during mitochondrial DNA PCR amplification. This paper is the first to fully sequence 29 paralogous nuclear DNA fragments that represent the entire mitochondrial genome. This is a surprising small number, because prior to this blast searches have suggested that nuclear DNA harbors between 400 to 1,500 paralogous mitochondrial DNA fragments. This possibility warrants careful experimental design and cautious interpretation of heteroplasmic results. Here we report the cloning and sequencing of numts loci, amplified from human tissue and rho zero (?0) cell line (control) with primers, known to amplify the mitochondrial genome. Our results indicate that multiple numts loci amplify simultaneously with the mitochondrial genome, increasing the load of pseudogene signal in PCR reactions. Further, the entire mitochondrial genome is represented by multiple copies of paralogous nuclear sequences. 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 which may co-amplify. The results show that mitochondrial heteroplasmy should be interpreted with caution to avoid inclusion of paralogous sequence variation as authentic data. Our 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 and is an important new reference tool.

Citation

BMC Genomics

Volume

7

Pub Type

Journals

Keywords

biomarkers, diagnostics, mitochondria, telomerase, validation

Citation

Parr, R. , Maki, J. , Reguly, B. , Dakubo, G. , Aguirre, A. , Wittock, R. , Robinson, K. , Jakupciak, J. and Thayer, R. (2006), The Pseudo-mitochondrial Genome Influences Mistakes in Heteroplasmy Interpretation, BMC Genomics (Accessed October 11, 2025)