title: Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.
abstract: 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/.
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei 10617, Taiwan.
authors.forename: Hsueh-Ting
authors.initials: HT
authors.lastname: Chu
authors.forename: William W L
authors.initials: WW
authors.lastname: Hsiao
authors.forename: Theresa T H
authors.initials: TT
authors.lastname: Tsao
authors.forename: Ching-Mao
authors.initials: CM
authors.lastname: Chang
authors.forename: Yen-Wenn
authors.initials: YW
authors.lastname: Liu
authors.forename: Chen-Chieh
authors.initials: CC
authors.lastname: Fan
authors.forename: Han
authors.initials: H
authors.lastname: Lin
authors.forename: Hen-Hong
authors.initials: HH
authors.lastname: Chang
authors.forename: Tze-Jung
authors.initials: TJ
authors.lastname: Yeh
authors.forename: Jen-Chih
authors.initials: JC
authors.lastname: Chen
authors.forename: Dun-Ming
authors.initials: DM
authors.lastname: Huang
authors.forename: Chaur-Chin
authors.initials: CC
authors.lastname: Chen
authors.forename: Cheng-Yan
authors.initials: CY
authors.lastname: Kao
mesh_terms: D000328:Adult; D002648:Child; D004272:DNA, Mitochondrial / Q000378:metabolism*; D030541:Databases, Genetic; D005260:Female; D015894:Genome, Human; D006801:Humans; D008297:Male; D008928:Mitochondria / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004272:DNA, Mitochondrial