Background: Mitochondrial dysfunction is associated with various aging diseases. The copy number of mtDNA in
human cells may therefore be a potential biomarker for diagnostics of aging. Here we propose a new
computational method for the accurate assessment of mtDNA copies from whole genome sequencing data.
Results: Two families of the human whole genome sequencing datasets from the HapMap and the 1000 Genomes
projects were used for the accurate counting of mitochondrial DNA copy numbers. The results revealed the
parental mitochondrial DNA copy numbers are significantly lower than that of their children in these samples.
There are 8%~21% more copies of mtDNA in samples from the children than from their parents. The experiment
demonstrated the possible correlations between the quantity of mitochondrial DNA and aging-related diseases.
Conclusions: Since the next-generation sequencing technology strives to deliver affordable and non-biased
sequencing results, accurate assessment of mtDNA copy numbers can be achieved effectively from the output of
whole genome sequencing. We implemented the method as a software package MitoCounter with the source
code and user’s guide available to the public at http://sourceforge.net/projects/mitocounter/.
