Quantitative assessment of mitochondrial DNA copies from whole genome sequencing
© Chu et al.; licensee BioMed Central Ltd. 2012
Published: 13 December 2012
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/.
In the past decade, quantitative real-time PCR assays were developed to estimate relative levels of mtDNA copy numbers in samples [2, 5, 6]. This approach measures the mtDNA copy number by determining the ratio of PCR amplicons to that of a single nuclear gene in experimental samples. The recent development of next-generation sequencing technology (NGS) revolutionized genomic studies and produced accurate whole genome sequencing (WGS) datasets . As shown in Figure 1b, the output from human whole genome sequencing consists of both nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) molecules, thus it is convenient to assess mtDNA copy number from WGS dataset and can be an alternative to real-time PCR assays.
Here we demonstrate a computational method for counting mtDNA copy number using WGS datasets. The three steps in the process are (1) typing of mtDNA, (2) separation of mtDNA reads, and (3) calculation of mtDNA count. We developed a freely available software package called MitoCounter for this purpose. MitoCounter can be used to calculate the average copy numbers of mtDNA molecules in the sequenced samples. Besides, the separated mtDNA reads provide further analysis of mtDNA heteroplasmy. The mtDNA heteroplasmy represents the mixture of individual mtDNA mutations. Heteroplasmy levels can alter the clinical penetrance of primary mtDNA diseases [8, 9].
A computational assay for counting mtDNA copies from a WGS dataset
Since the library construction bias is minimized with the next-generation sequencing platform , both mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) are sequenced together with equal opportunities. The output dataset comprises a mixture of mtDNA reads and nuDNA reads. Let the total number of nucleotide bases in the nuclear genome be 2N (for diploid chromosomes) and the number of bases in a mitochondrial DNA is M. Then the summation of nucleotide bases in the entire human genome is 2N+kM, where k is the number of mtDNA copies. The numbers of reads from nuDNA and the number of reads from mtDNA should reflect the ratio of 2N:kM.
where mtBases is the total bases of sequenced reads from mtDNA and allBases is total bases of all sequenced reads from the output of a WGS procedure.
The equation for counting mtDNA copies is not suitable for plants (e.g. Arabidopsis) since their mtDNA sequences may contain segments of nuclear DNA. Besides, there are usually other DNA molecules in their cells, such as chloroplast genome and plasmid genome.
In order to precisely separate mtDNA reads from a WGS dataset, it is necessary to determine the genotype of the mitochondrial genome first. We designed a program WgsMitoAssembler to identify the homoplasmic sequences, which present the inherent mutations in most of mtDNA molecules. The program WgsMitoAssembler is a guided assembler, and it requires a reference mitochondrial sequence which is used to choose a beginning read and an ending read from the entire WGS dataset. We use the reference mtDNA sequence (GenBank: NC_001807.4) for the purpose. We then search for best candidate reads which can extend the beginning read from the 3' end to the 5' end until the ending read is met.
Results and discussion
Parental mtDNA samples have less copy numbers
Typing of mtDNA from whole genome sequencing samples
Counts of mtDNA from whole genome sequencing samples
For the counting results of these WGS samples (Additional file 2 and 3), ANOVA analysis revealed significant differences among the mtDNA counts within each family group: for YOR009, F(2,69) = 916.01, p = 2.06E-50 and for CEPH1463, F(2,169) = 58.75, p = 7.26632E-19. It showed that the offspring had 8%~23% more mtDNA than their parents in these samples. Although we did not investigate the possible artefacts caused by sequencing procedures, the results consistently demonstrated that there are more mtDNA sequences within younger persons' lymphocyte cells.
Many studies suggested that mitochondrial functions become defective as we age. Recent findings suggests that structural changes in mitochondria, including increased mitochondrial fragmentation and decreased mitochondrial fusion, are critical factors associated with mitochondrial dysfunction and cell death in aging and neurodegenerative diseases [13, 14]. Therefore, the proposed quantitative analysis of mtDNA can help to further elucidate the dynamics of mitochondrial diseases. It is expected that cost for sequencing personal whole genome will be less than $1000 in the near future. For the purpose of counting mitochondrial DNA, it only requires a low coverage of the whole genome and the cost may be further reduced to $50. The cost-effectiveness of the procedure makes the proposed method of counting mitochondrial DNA as a useful diagnostic tool to study aging and aging-related diseases for individuals.
Availability and requirements
In the MitoCounter software package, both the programs WgsMitoAssembler and WgsMitoCounter were implemented in C# with the .NET Framework which can be run on 64-bit Windows. The program WgsMitoCounter requires paired-end WGS datasets from Illumina sequencing platform. The MitoCounter software with a user manual is available at the Web site: http://sourceforge.net/projects/mitocounter/
We thank the members in the Bioinformatics Lab, NTU, for valuable discussions and useful insights. We thank C. S. Chiou, C. H. Chan and C. F. Chang for comments and discussion. We thank Flora Kao for editing and proofreading.
This article has been published as part of BMC Genomics Volume 13 Supplement 7, 2012: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/13/S7.
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