Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.
Journal
BMC genomics
Journal Volume
13 Suppl 7
Date Issued
2012
Author(s)
Chu, H.T.
Abstract
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. 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. 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/.
SDGs
Other Subjects
mitochondrial DNA; adult; article; child; computer program; DNA sequence; female; genetic database; genetics; human; human genome; male; metabolism; mitochondrion; Adult; Child; Databases, Genetic; DNA, Mitochondrial; Female; Genome, Human; Humans; Male; Mitochondria; Sequence Analysis, DNA; Software
Type
journal article