A microarray system for genotyping 150 single nucleotide polymorphisms in the coding region of human mitochondrial DNA

Evaluating heteroplasmic variations of the mitochondrial genome from whole genome sequencing data

BACKGROUND

Detecting heteroplasmic variations in the mitochondrial genome can help identify potential pathogenic possibilities, which is significant for disease prevention. The development of next-generation sequencing changed the quantification of mitochondrial DNA (mtDNA) heteroplasmy from scanning limited recorded points to the entire mitochondrial genome. However, due to the presence of nuclear mtDNA homologous sequences (nuMTs), maximally retaining real variations while excluding falsest heteroplasmic variations from nuMTs and sequencing errors presents a dilemma.

RESULTS

Herein, we used an improved method for detecting low-frequency mtDNA heteroplasmic variations from whole genome sequencing data, including point variations and short-fragment length alterations, and evaluated the effect of this method. A two-step alignment was designed and performed to accelerate data processing, to obtain and retain the true mtDNA reads and to eliminate most nuMTs reads. After analyzing whole genome sequencing data of K562 and GM12878 cells, ~90% of heteroplasmic point variations were identified in MitoMap. The results were consistent with the results of an amplification refractory mutation system qPCR. Many linkages of the detected heteroplasmy variations were also discovered.

CONCLUSIONS

Our improved method is a simple, efficient and accurate way to mine mitochondrial low-frequency heteroplasmic variations from whole genome sequencing data. By evaluating the highest misalignment possibility caused by the remaining nuMTs-like reads and sequencing errors, our procedure can detect mtDNA heteroplasmic variations whose heteroplasmy frequencies are as low as 0.2%.

Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations

The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.

Differentiating between monozygotic twins through next-generation mitochondrial genome sequencing

Monozygotic (MZ) twins, considered to be genetically identical, cannot be distinguished from one another by standard forensic DNA testing. A recent study employed whole genome sequencing to identify extremely rare mutations and reported that mutation analysis could be used to differentiate between MZ twins. Compared with nuclear DNA, mitochondrial DNA (mtDNA) has higher mutation rates; therefore, minor differences theoretically exist in MZ twins' mitochondrial genome (mtGenome). However, conventional Sanger-type sequencing (STS) is neither amenable to, nor feasible for, the detection of low-level sequence variants. The recent introduction of massively parallel sequencing (MPS) has the capability to sequence many targeted regions of multiple samples simultaneously with desirable depth of coverage. Thus, the aim of this study was to assess whether full mtGenome sequencing analysis can be used to differentiate between MZ twins. Ten sets of MZ twins provided blood samples that underwent extraction, quantification, mtDNA enrichment, library preparation, and ultra-deep sequencing. Point heteroplasmies were observed in eight sets of MZ twins, and a single nucleotide variant (nt15301) was detected in five sets of MZ twins. Thus, this study demonstrates that ultra-deep mtGenome sequencing could be used to differentiate between MZ twins.

mitoSAVE: mitochondrial sequence analysis of variants in Excel

The mitochondrial genome (mtGenome) contains genetic information amenable to numerous applications such as medical research, population and evolutionary studies, and human identity testing. However, inconsistent nomenclature assignment makes haplotype comparison difficult and can lead to false exclusion of potentially useful profiles. Massively Parallel Sequencing (MPS) is a platform for sequencing large datasets and potentially whole populations with relative ease. However, the data generated are not easily parsed and interpreted. With this in mind, mitoSAVE has been developed to enable fast conversion of Variant Call Format (VCF) files. mitoSAVE is an Excel-based workbook that converts data within the VCF into mtDNA haplotypes using phylogenetically-established nomenclature as well as rule-based alignments consistent with current forensic standards. mitoSAVE is formatted for human mitochondrial genome; however, it can easily be adapted to support other reasonably small genomes.

Development of a multiplex PCR system of 59 mitochondrial SNPs and genetic analysis in Chinese population

The analysis of SNPs located on the mitochondrial DNA can provide information on maternal genetics. In the present study, a set of 59 SNPs were detected simultaneously using three multiplex allele-specific PCR and subsequent CE. Allele-specific primers were designed with different sizes to allow for specifically amplified paired alleles in the same reaction. An allelic ladder based on reference alleles was also created to maintain high-quality analysis standard. Samples from 400 unrelated individuals (200 of Han population and 200 of Uyghur population, China) were successfully analyzed and assigned into 106 relevant haplotypes, resulting in a discrimination power of 98.5%. The haplotype diversity was 0.978 for Han and 0.972 for Uyghur, respectively. Pairwise comparison of haplotype frequency distributions showed significant difference across ethnicities. These results suggest that the 59-SNP PCR system is a reliable, rapid, and economical method for large-scale screening of mitochondrial DNA variation, adding a new aspect for forensic individual identification.

Molecular cytogenetics: making it safe for human embryonic stem cells to enter the clinic

Regenerative therapies based on transplantation of cells derived from human embryonic stem cells (hESC) are currently being prepared for clinical trials. Unfortunately, recent evidence indicates that many kinds of changes can occur to hESC during expansion in culture, and alterations to the growth control mechanisms may be required to establish hESC lines at all. Changes in the genome and epigenome can affect the validity of in vitro and animal studies, and put transplant recipients at increased risk of cancer. New molecular cytogenetic technologies enable us to examine the whole human genome with ever-finer resolution. This review describes several techniques for whole-genome analysis and the information they can provide about hESC lines. Adoption of high-resolution genotyping into routine characterization may prevent highly discouraging clinical outcomes.

Mitochondrial gene profiling: translational perspectives

The last decade has witnessed the development of multiple microarray platforms designed to study, in a comprehensive fashion, the expression and sequence of both mitochondrial and nuclear genes that encode mitochondrial proteins. Mitochondrial dysfunction has been implicated in a number of severe medical conditions including cancer, metabolic diseases (i.e., cardiovascular, diabetes and obesity) and neurodegenerative disorders and it is responsible for the adverse effects of numerous drugs. Profiling of the genetic and genomic status of mitochondria with focused microarrays offers the promise of rapidly and robustly identifying novel biomarkers for early disease diagnoses and prognoses, predicting of drug safety, liability, and selecting and stratifying of patients in clinical trials.

Titanic's unknown child: the critical role of the mitochondrial DNA coding region in a re-identification effort

This report describes a re-examination of the remains of a young male child recovered in the Northwest Atlantic following the loss of the Royal Mail Ship Titanic in 1912 and buried as an unknown in Halifax, Nova Scotia shortly thereafter. Following exhumation of the grave in 2001, mitochondrial DNA (mtDNA) hypervariable region 1 sequencing and odontological examination of the extremely limited skeletal remains resulted in the identification of the child as Eino Viljami Panula, a 13-month-old Finnish boy. This paper details recent and more extensive mitochondrial genome analyses that indicate the remains are instead most likely those of an English child, Sidney Leslie Goodwin. The case demonstrates the benefit of targeted mtDNA coding region typing in difficult forensic cases, and highlights the need for entire mtDNA sequence databases appropriate for forensic use.

SNaPshot minisequencing to resolve mitochondrial macro-haplogroups found in Africa

African mitochondrial DNA (mtDNA) haplogroups are divided into seven macro-haplogroups (L0'1'2'3'4'5'6), while the rest of the world's lineages are classified as subgroups of macro-haplogroups M, N and R. The most common approach to characterizing mtDNA variation is the sequencing of hypervariable segments I and II of the non-coding control region of the molecule. Given the higher mutation rate within the control region compared with the coding regions of the molecule, recurrent mutations in the former can sometimes hide possible phylogenetic structure. The incorporation of haplogroup-defining coding region mutations has helped in overcoming this limitation. By judiciously selecting 14 coding region SNPs and incorporating them into a multiplex minisequencing assay we were able to resolve mtDNA sequences from some sub-Saharan African populations into ten macro-haplogroups (L0-L6, M, N and R). We tested the efficacy of the panel by screening 699 individuals, consisting mostly of Khoe-San, Bantu speakers and individuals with mixed ancestries (Coloreds) and found no inconsistencies compared with hypervariable segment sequencing results. The panel provided a fast and efficient means of classifying mtDNA into the ten mitochondrial macro-haplogroups and provided a reliable screening to distinguish African from non-African-derived mtDNA lineages.

Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays

BACKGROUND

Nucleic acid detection based on ligation reaction or single nucleotide extension of ssDNA probes followed by tag microarray hybridization provides an accurate and sensitive detection tool for various diagnostic purposes. Since microarray quality is crucial for reliable detection, these methods can benefit from correcting for microarray artefacts using specifically adapted techniques.

FINDINGS

Here we demonstrate the application of a per-spot hybridization control oligonucleotide probe and a novel way of computing normalization for tag array data. The method takes into account the absolute value of the detection probe signal and the variability in the control probe signal to significantly alleviate problems caused by artefacts and noise on low quality microarrays.

CONCLUSIONS

Diagnostic microarray platforms require experimental and computational tools to enable efficient correction of array artefacts. The techniques presented here improve the signal to noise ratio and help in determining true positives with better statistical significance and in allowing the use of arrays with poor quality that would otherwise be discarded.

Detection of known base substitution mutations in human mitochondrial DNA of MERRF and MELAS by biochip technology

We developed a DNA biochip specialized for detection of known base substitution mutations in mitochondrial DNA causing mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) and myoclonic epilepsy associated with ragged-red fibers (MERRF). A set of probes sharing a given allele-specific sequence with a single base substitution near the middle of the sequence was covalently immobilized. Cy5-labeled DNA targets were amplified from sample DNAs containing 31 potential MELAS and/or MERRF mutations by a multiplex PCR method. Detection parameters for the DNA biochip-based assay were accordingly optimized. Seven clinically confirmed patients with MELAS, 5 patients with MERRF, 1 suspected MERRF case and 25 healthy controls were tested using the DNA biochip. For discriminating of homoplasmic and heteroplasmic point mutations in mtDNA, a diagnostic factor based on the ratio between the hybridization signals from the reference and test targets with each probe was used. The results showed that all the cases with MELAS had a causal heteroplasmic A3243G tRNA(Leu(UUR)) mutation. In the MERRF patients, four cases were found to be a homoplasmic A8344G tRNA(Lys) mutation and one case was a heteroplasmic T8356C tRNA(Lys) mutation. None of the healthy controls carried the potential mutations. The results of the DNA biochip were completely consistent with those by DNA sequencing. Thus, the DNA biochip would potentially become a valuable tool in clinical specific screening of the mtDNA point mutations associated with MELAS and/or MERRF syndrome.

[Detection of mtDNA coding region variants using mAPLP in Han, Miao and Tujia populations from Hunan Province]

To find a rapid single nucleotide polymorphism (SNP) loci typing method in the mitochondrial DNA (mtDNA) coding regions, we genotyped 16 SNP loci in the mitochondrial DNA coding region in Han, Miao and Tujia populations by the multiplex-amplified product-length polymorphism (mAPLP) technique. This method generates allele-specific fragments that are different in length through PCR amplification using allele-specific forward (or reverse) primers different in size and a common reverse (or forward) primer. Results showed that both of the allelic frequency of 3970T in Han and Tujia populations were 17%, which were significantly different from that of in the Miao population (P0.01). The allelic frequency of 8020A in Han population was 6% , which was different from that of in the Miao and Tujia populations (P0.05) . In all of 300 samples, a total of 45 different haplotypes were identified, 12 of which were found in all the three populations, 10 were shared by two populations and 23 haplotypes existed only in one of the populations. Among these 23 haplotypes, 8, 6 and 12 haplotypes were exclusively observed in the Han, Miao and Tujia populations, respectively.

Multiplex mutagenically separated polymerase chain reaction assay for rapid detection of human mitochondrial DNA variations in coding area

Recently, it has been recognized that information in the mitochondrial DNA (mtDNA) coding region can provide additional forensic discrimination with respect to the standard typing of the D-loop region, increasing the forensic power of mtDNA testing, which is sometimes rather limited. In the present study, we simultaneously typed ten single nucleotide polymorphisms (SNP) in the coding region by use of mutagenically separated polymerase chain reaction (MS-PCR) in the Chinese Chengdu population. This technique, in which different-size allele-specific primers were used, specifically amplified both alleles of mtDNA in the same reaction. Subsequent gel electrophoresis showed ten of the allelic products of different loci. Using multiplex MS-PCR, 30 primers were added simultaneously into one reaction tube to identify ten SNPs. The mtDNA variations of 160 individuals from the Chinese Chengdu population were examined and classified into 18 haplotypes. The multiplex MS-PCR method is suitable for large-scale screening studies of mtDNA variability because it is both rapid and economical.