2013年4月23日 星期二

[論文發表] Quantitative assessment of mitochondrial DNA copies from whole genome sequencing (SCI)


Proceedings

Quantitative assessment of mitochondrial DNA copies from whole genome sequencing

Hsueh-Ting Chu12William WL Hsiao34Theresa TH Tsao5Ching-Mao Chang6,Yen-Wenn Liu8Chen-Chieh Fan5Han Lin5Hen-Hong Chang67Tze-Jung Yeh9,Jen-Chih Chen9Dun-Ming Huang2Chaur-Chin Chen10 and Cheng-Yan Kao5*






1Department of Biomedical informatics, Asia University, Taichung 41354, Taiwan
2Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan
3BCCDC Public Health Microbiology & Reference Laboratory, Vancouver, BC, V5Z 4R4, Canada
4Department of Pathology and Laboratory Medicine, Vancouver, BC, V5Z 4R4, Canada
5Department of Computer Science and Information Engineering, National Taiwan University, Taipei 10617, Taiwan
6Graduate Institute of Clinical Medical Science, Chang Gung University, Taoyuan 33302, Taiwan
7Center for Traditional Chinese Medicine, Chang Gung Memorial Hospital at Taoyuan, Chang Gung Medical Foundation, Taoyuan 33302, Taiwan
8Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan
9Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
10Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan
Email: Hsueh-Ting Chu chu@live.asia.edu.tw - William WL Hsiaowilliam.hsiao@gmail.com - Theresa TH Tsao postergrey@gmail.com - Ching-Mao Changmagicbjp@gmail.com - Yen-Wenn Liu skywenn@gmail.com - Chen-Chieh Fanfanent@gmail.com - Han Lin hotdogee@gmail.com - Hen-Hong Changtcmchh@mail.cgu.edu.tw - Tze-Jung Yeh judyyah@gmail.com - Jen-Chih Chenjchchen@ntu.edu.tw - Dun-Ming Huang chobitshuang@yahoo.com.tw - Chaur-Chin Chen cchen@cs.nthu.edu.tw - Cheng-Yan Kao cykao@csie.ntu.edu.tw










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

The electronic version of this article is the complete one and can be found online at:http://www.biomedcentral.com/1471-2164/13/S5/S5

Published:13 December 2012
© 2012 Chu et al.; licensee BioMed Central Ltd. 

http://www.biomedcentral.com/1471-2164/13/S7/S5










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.