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This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology

Open Access Proceedings

Quantitative assessment of mitochondrial DNA copies from whole genome sequencing

Hsueh-Ting Chu12, William WL Hsiao34, Theresa TH Tsao5, Ching-Mao Chang6, Yen-Wenn Liu8, Chen-Chieh Fan5, Han Lin5, Hen-Hong Chang67, Tze-Jung Yeh9, Jen-Chih Chen9, Dun-Ming Huang2, Chaur-Chin Chen10 and Cheng-Yan Kao5*

Author Affiliations

1 Department of Biomedical informatics, Asia University, Taichung 41354, Taiwan

2 Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan

3 BCCDC Public Health Microbiology & Reference Laboratory, Vancouver, BC, V5Z 4R4, Canada

4 Department of Pathology and Laboratory Medicine, Vancouver, BC, V5Z 4R4, Canada

5 Department of Computer Science and Information Engineering, National Taiwan University, Taipei 10617, Taiwan

6 Graduate Institute of Clinical Medical Science, Chang Gung University, Taoyuan 33302, Taiwan

7 Center for Traditional Chinese Medicine, Chang Gung Memorial Hospital at Taoyuan, Chang Gung Medical Foundation, Taoyuan 33302, Taiwan

8 Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan

9 Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan

10 Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan

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BMC Genomics 2012, 13(Suppl 7):S5  doi:10.1186/1471-2164-13-S7-S5

Published: 13 December 2012

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/ webcite.