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1.
《Forensic science international. Genetics》2014,8(6):632-639
Insights into the human mitochondrial phylogeny have been primarily achieved by sequencing full mitochondrial genomes (mtGenomes). In forensic genetics (partial) mtGenome information can be used to assign haplotypes to their phylogenetic backgrounds, which may, in turn, have characteristic geographic distributions that would offer useful information in a forensic case. In addition and perhaps even more relevant in the forensic context, haplogroup-specific patterns of mutations form the basis for quality control of mtDNA sequences. The current method for establishing (partial) mtDNA haplotypes is Sanger-type sequencing (STS), which is laborious, time-consuming, and expensive. With the emergence of Next Generation Sequencing (NGS) technologies, the body of available mtDNA data can potentially be extended much more quickly and cost-efficiently. Customized chemistries, laboratory workflows and data analysis packages could support the community and increase the utility of mtDNA analysis in forensics. We have evaluated the performance of mtGenome sequencing using the Personal Genome Machine (PGM) and compared the resulting haplotypes directly with conventional Sanger-type sequencing. A total of 64 mtGenomes (>1 million bases) were established that yielded high concordance with the corresponding STS haplotypes (<0.02% differences). About two-thirds of the differences were observed in or around homopolymeric sequence stretches. In addition, the sequence alignment algorithm employed to align NGS reads played a significant role in the analysis of the data and the resulting mtDNA haplotypes. Further development of alignment software would be desirable to facilitate the application of NGS in mtDNA forensic genetics. 相似文献
2.
The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the question of human identification. Previous recommendations published in 2000 addressed the analysis and interpretation of mitochondrial DNA (mtDNA) in forensic casework. While the foundations set forth in the earlier recommendations still apply, new approaches to the quality control, alignment and nomenclature of mitochondrial sequences, as well as the establishment of mtDNA reference population databases, have been developed. Here, we describe these developments and discuss their application to both mtDNA casework and mtDNA reference population databasing applications. While the generation of mtDNA for forensic casework has always been guided by specific standards, it is now well-established that data of the same quality are required for the mtDNA reference population data used to assess the statistical weight of the evidence. As a result, we introduce guidelines regarding sequence generation, as well as quality control measures based on the known worldwide mtDNA phylogeny, that can be applied to ensure the highest quality population data possible. For both casework and reference population databasing applications, the alignment and nomenclature of haplotypes is revised here and the phylogenetic alignment proffered as acceptable standard. In addition, the interpretation of heteroplasmy in the forensic context is updated, and the utility of alignment-free database searches for unbiased probability estimates is highlighted. Finally, we discuss statistical issues and define minimal standards for mtDNA database searches. 相似文献
3.
Resolution of mitochondrial (mt) DNA heteroplasmy is now possible when applying a massively parallel sequencing (MPS) approach, including minor components down to 1%. However, reporting thresholds and interpretation criteria will need to be established for calling heteroplasmic variants that address a number of important topics, one of which is DNA damage. We assessed the impact of increasing amounts of DNA damage on the interpretation of minor component sequence variants in the mtDNA control region, including low-level mixed sites. A passive approach was used to evaluate the impact of storage conditions, and an active approach was employed to accelerate the process of hydrolytic damage (for example, replication errors associated with depurination events). The patterns of damage were compared and assessed in relation to damage typically encountered in poor quality samples. As expected, the number of miscoding lesions increased as conditions worsened. Single nucleotide polymorphisms (SNPs) associated with miscoding lesions were indistinguishable from innate heteroplasmy and were most often observed as 1–2% of the total sequencing reads. Numerous examples of miscoding lesions above 2% were identified, including two complete changes in the nucleotide sequence, presenting a challenge when assessing the placement of reporting thresholds for heteroplasmy. To mitigate the impact, replication of miscoding lesions was not observed in stored samples, and was rarely seen in data associated with accelerated hydrolysis. In addition, a significant decrease in the expected transition:transversion ratio was observed, providing a useful tool for predicting the presence of damage-induced lesions. The results of this study directly impact MPS analysis of minor sequence variants from poorly preserved DNA extracts, and when biological samples have been exposed to agents that induce DNA damage. These findings are particularly relevant to clinical and forensic investigations. 相似文献
4.
Tagliabracci A Turchi C Buscemi L Sassaroli C 《International journal of legal medicine》2001,114(4-5):224-228
Mitochondrial DNA sequences of the hypervariable regions HVI and HVII were analysed in 83 Caucasians living in central Italy
to expand the database for forensic identification purposes, and 75 different haplotypes resulting from 62 polymorphic positions
in HVI and 44 in HVII were observed. The most frequent haplotype (263G, 309.1C, 315.1C) was shared by 7 individuals, 2 haplotypes
were shared by 2 individuals, and 72 were unique. The genetic diversity was found to be 0.99 and the random match probability
1.9%. A condition of sequence heteroplasmy was found in only one case at nt 16311, whereas a length heteroplasmy was found
in the homopolymeric stretch of cytosines 303–315. Our results indicate that in direct sequencing beyond the poly-cytosine
stretch, the overlap is due to length heteroplasmy, whereas the blurred signal occurs when the stretch is composed of more
than 10 cytosines.
Received: 14 February 2000 / Accepted: 23 May 2000 相似文献
5.
J. Hühne H. Pfeiffer K. Waterkamp B. Brinkmann 《International journal of legal medicine》1999,112(3):172-175
The sequences of the hypervariable region 1 (HV1) of the mitochondrial DNA control region from multiple hair shafts from
10 unrelated individuals were compared to determine the frequency of differences in hairs from one individual. The extraction
method described herein showed an average success rate of 67% for all 150 hair shafts tested in HV1. The mtDNA sequences from
the hair shafts matched the sequences from the corresponding blood and saliva samples taken from the same donor and no evidence
of heteroplasmy was found. The results emphasize the reliability of DNA extraction and mtDNA typing from human hair shafts
for forensic purposes.
Received: 16 July 1998 / Received in revised form: 31 August 1998 相似文献
6.
Mashima Y Nagano M Funayama T Zhang Q Egashira T Kudho J Shimizu N Oguchi Y 《Clinical biochemistry》2004,37(4):268-276
PURPOSE: To quantify the degree of heteroplasmy of a mitochondrial DNA (mtDNA) mutation in Leber's hereditary optic neuropathy (LHON) a biplex Invader assay was applied. METHODS: To determine the optimum condition for the Invader assay, mtDNAs were assayed in various amounts of total DNA in 1-4-h incubations at 63 degrees C. To evaluate the suitability of the Invader assay to detect the three mutations, G3460A, G11778A, and T14484C, 10 ng of DNAs from 224 patients with bilateral optic atrophy was assayed. To quantify mtDNA heteroplasmy, a standard curve of known mixture ratios of mutation against calculation by the Invader assay was constructed. Seventy-two of the 224 patients had one of the three mutations, which corresponded with the mutation detected earlier by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis. The percentages of mutant mtDNAs were calculated by the Invader assay in five heteroplasmic families, including 30 individuals with the G11778A mutation. The results were compared with those calculated earlier by labeled polymerase chain reaction followed by single-strand conformation polymorphism (PCR-SSCP) analysis. RESULTS: In 1-8 ng of DNA, the fluorescence intensity increased near linearly during a 4-h assay. With more than 16 ng of DNA, the intensities were saturated even at the 2-h assay. A linear relationship was observed between the results obtained from separate mixtures and from the Invader assay analysis. Because two fluorescent intensities are not always the same, one of the two intensities was modified to adjust to that of the other. Complete concordance was observed between PCR-RFLP analysis and Invader assay genotyping for the 224 patients. Results of percentage of heteroplasmy in five LHON families obtained by the Invader assay were consistent with those by the PCR-SSCP analysis. CONCLUSIONS: Invader assay is a simple, rapid, and reliable method of genotyping mtDNA mutations as well as quantifying heteroplasmy simultaneously under optimum conditions. 相似文献
7.
Mitochondrial DNA(mtDNA) is particularly prone to oxidation due to the lack of histones and a deficient mismatch repair system.This explains an increased mutation rate of mtDNA that results in heteroplasmy,e.g.,the coexistence of the mutant and wild-type mtDNA molecules within the same mitochondrion.In diabetes mellitus,glycotoxicity,advanced oxidative stress,collagen cross-linking,and accumulation of lipid peroxides in foam macrophage cells and arterial wall cells may significantly decrease the mutation threshold required for mitochondrial dysfunction,which in turn further contributes to the oxidative damage of the diabetic vascular wall,endothelial dysfunc-tion,and atherosclerosis. 相似文献
8.
Emma F Pizzini C Tessa A Di Giandomenico S Onetti-Muda A Santorelli FM Bertini E Rizzoni G 《Pediatric nephrology (Berlin, Germany)》2006,21(3):355-360
Kearns-Sayre syndrome (KSS) is a mitochondrial disease caused by large deletions in mitochondrial DNA (mtDNA). In most patients the disease is characterized by mtDNA heteroplasmy, where a mixture of wild-type and mutated mtDNA co-exist within cells in variable proportion, modulating the severity of the phenotype in different tissues. We report on the case of a 14-year-old child with classical symptoms of KSS and a renal phenotype characterized by hypokalaemic alkalosis, hypomagnesaemia, hyperreninaemia, hyperaldosteronism and nephrocalcinosis, resembling Bartter syndrome. Analysis of mtDNA demonstrated an 8,661 bp deletion involving eight mitochondrial genes. Uneven degrees of mtDNA heteroplasmy were demonstrated in several tissues, ranging from 24% to 60% of deleted/total mtDNA. Variable degrees of expression of mitochondrial enzymes were also found in biopsy specimens of renal and skeletal muscle by histocytochemistry. In particular, preserved cytochrome c oxidase was observed in tubular structures within medullary rays. It is proposed that a "Bartter-like" phenotype can arise in some patients with KSS as a result of heteroplasmy. In these cases aldosterone-responsive tubular structures have been spared during renal embryogenesis, allowing for the development of hypokalaemic alkalosis in response to salt and water losses from the more damaged tubular segments. 相似文献
9.
Elena Schlapakow Viktoriya Peeva Gábor Zsurka Monika Jeub Bettina Wabbels Cornelia Kornblum Wolfram S. Kunz 《Neuromuscular disorders : NMD》2019,29(5):358-367
Chronic progressive external ophthalmoplegia (CPEO) is a frequent clinical manifestation of disorders caused by pathogenic mitochondrial DNA mutations. However, for diagnostic purposes skeletal muscle tissue is used, since extraocular muscle tissue is usually not available for work-up. In the present study we aimed to identify causative factors that are responsible for extraocular muscle to be primarily affected in CPEO. We performed comparative histochemical and molecular genetic analyses of extraocular muscle and skeletal muscle single fibers in a case of isolated CPEO caused by the heteroplasmic m.5667G>A mutation in the mitochondrial tRNAAsn gene (MT-TN). Histochemical analyses revealed higher proportion of cytochrome c oxidase deficient fibers in extraocular muscle (41%) compared to skeletal muscle (10%). However, genetic analyses of single fibers revealed no significant difference either in the mutation loads between extraocular muscle and skeletal muscle cytochrome c oxidase deficient single fibers (extraocular muscle 86% ± 4.6%; skeletal muscle 87.8 %± 5.7%, p = 0.246) nor in the mutation threshold (extraocular muscle 74% ± 3%; skeletal muscle 74% ± 4%). We hypothesize that higher proportion of cytochrome c oxidase deficient fibers in extraocular muscle compared to skeletal muscle might be due to facilitated segregation of the m.5667G>A mutation into extraocular muscle, which may explain the preferential ocular manifestation and clinically isolated CPEO. 相似文献
10.
Mitochondrial DNA deletion with Kearns Sayre syndrome in a child with Addison disease 总被引:3,自引:0,他引:3
R. G. Boles T. Roe D. Senadheera V. Mahnovski L. J. C. Wong 《European journal of pediatrics》1998,157(8):643-647
Kearns Sayre syndrome (KSS) is a multisystem disorder with a confounding variety of clinical manifestations, including ocular
myopathy, pigmentary retinopathy, heart block and ataxia. Endocrinopathies are common in KSS, including growth hormone deficiency,
hypogonadism, diabetes mellitus and hypoparathyroidism. A variety of deletions of mitochondrial DNA (mtDNA) are found in
most cases. We report on a 5-year-old boy with Addison disease in whom further investigation revealed a 4.9 kilobase mtDNA
deletion and KSS. Later he developed severe lactic acidosis and expired.
Conclusion The degree of mutant mtDNA heteroplasmy in various tissues on autopsy did not correlate well with the clinical manifestations,
although this may be due at least in part to replacement with other tissue types. Our report is the first of non-autoimmune
Addison disease in KSS and patients with KSS should be evaluated for adrenal insufficiency. Early recognition of adrenal insufficiency
is crucial to prevent mortality from this cause.
Received: 1 October 1997 / Accepted: 11 March 1998 相似文献