Novel mitochondrial DNA mutations associated with myopathy, cardiomyopathy, renal failure, and deafness

Patients with mitochondrial disease usually manifest multisystemic dysfunction with a broad clinical spectrum. When the tests for common mitochondrial DNA (mtDNA) point mutations are negative and the mtDNA defects are still hypothesized, it is necessary to screen the entire mitochondrial genome for unknown mutations in order to confirm the diagnosis. We report an 8-year-old girl who had a long history of ragged-red fiber myopathy, short stature, and deafness, who ultimately developed renal failure and fatal cardiac dysfunction. Respiratory chain enzyme analysis on muscle biopsy revealed deficiency in complexes I, II/III, and IV. Whole mitochondrial genome sequencing analysis was performed. Three novel changes: homoplasmic 15458T > C and 15519T > C in cytochrome b, and a near homoplasmic 5783G > A in tRNA(cys), were found in the proband in various tissues. Her mother and asymptomatic sibling also carry the two homoplasmic mutations and the heteroplasmic 5783G > A mutation in blood, hair follicles, and buccal cells, at lower percentage. The 5783G > A mutation occurs at the T arm of tRNA(cys), resulting in the disruption of the stem structure, which may reduce the stability of the tRNA. 15458T > C changes an amino acid serine to proline at a conserved alpha-helix, which may force the helix to bend. These two mutations may have pathogenic significance. This case emphasizes the importance of pursuing more extensive mutational analysis of mtDNA in the absence of common mtDNA point mutations or large deletions, when there is a high suspicion of a mitochondrial disorder.     

Contrasting phenotypes in three patients with novel mutations in mitochondrial tRNA genes

We studied three patients, each harboring a novel mutation at a highly conserved position in a different mitochondrial tRNA gene. The mutation in patient 1 (T5543C) was associated with isolated mitochondrial myopathy, and occurred in the anticodon loop of tRNA(Trp). In patient 2, with mitochondrial myopathy and marked retinopathy, the mutation (G14710A) resulted in an anticodon swap (Glu to Lys) in tRNA(Glu). Patient 3, who manifested mitochondrial encephalomyopathy and moderate retinal dysfunction, harbored a mutation (C3287A) in the TpsiC loop of tRNA(Leu(UUR)). The mutations were heteroplasmic in muscle in all cases, and sporadic in two cases. PCR-RFLP analysis in all patients showed much higher amounts of mutated mtDNA in affected tissue (muscle) than unaffected tissue (blood), and significantly higher levels of mutated mtDNA in cytochrome c oxidase (COX)-negative muscle fibers than in COX-positive fibers, confirming the pathogenicity of these mutations. The mutation was also detected in single hair roots from all three patients, indicating that each mutation must have arisen early in embryonic development or in maternal germ cells. This suggests that individual hair root analyses may reflect a wider tissue distribution of mutated mtDNA than is clinically apparent, and might be useful in predicting prognosis and, perhaps, the risk of transmitting the mutation to offspring. Our data suggest a correlation between clinical phenotype and distribution of mutated mtDNA in muscle versus hair roots. Furthermore, the high threshold for phenotypic expression in single muscle fibers (92-96%) suggests that therapies may only need to increase the percentage of wild-type mtDNA by a small amount to be beneficial.     

2型糖尿病患者线粒体基因8个突变位点的研究

目的：探讨线粒体DNA tRNA Leu (UUR)基因及其相邻的ND1基因8个位点的突变与2型糖尿病的关系。 方法： 采用聚合酶链反应-限制性片段长度多态性（PCR-RFLP）的分析方法，对174例2型糖尿病患者和207名健康对照的mtDNA的3 243、3 256、3 290、3 316、3 394、3 421、3 426、3 460和3 593共9个已报道的突变位点同时进行筛选，并采用测序、反向斑点杂交和基因芯片进行方法学比较和确证，对检出的突变位点采用DNASTAR和Antherprot软件进行分析。 结果： 糖尿病组检出3 316(G→A) 突变5例(2.9%)，其中2例为多个位点突变：1例伴随3 256(C→T)和3 688(G→C)，另1例伴随3 606(A→G)；3 394(T→C)突变4例(2.3%)，3 593(T→C)、3 290(T→C)和3 618(T→C)突变各1例(0.6%)； 其中3 606(A→G)、3 618(T→C)和3 688(G→C) 为新突变位点，GenBank登录号为DQ092356；对照组只检出3 316(G→A)突变1例(0.5%)。两组间仅3 394(T→C) 突变率差异显著(P<0.05)。以上8个突变位点的测序、反向斑点杂交和基因芯片检测结果完全一致。3 606(A→G)为Leu的无意义突变，3 618(T→C)为Phe的无意义突变，3 688(G→C)为有意义突变，Ala→Pro,导致ND1蛋白的二级结构发生改变。 结论： 线粒体DNA ND1基因3 316(G→A)突变伴随3 688(G→C)突变，3 394(T→C) 突变可能与2型糖尿病发病有关。     

Clinical features of MELAS and its relation with A3243G gene point mutation

Mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS) mostly occur in children. The point mutation A3243G of mitochondrial DNA (mtDNA) may work as a specific bio-marker for mitochondrial disorders. The related clinical features, however, may vary among individuals. This study therefore investigated the relation between MELAS clinical features and point mutation A3243G of mtDNA, in an attempt to provide further evidences for genetic diagnosis of MELAS. Children with MELAS-like syndromes were tested for both blood lactate level and point mutation A3243G of mtDNA. Further family study was performed by mtDNA mutation screening at the same loci for those who had positive gene mutation at A3243G loci. Those who were negative for A3243G point mutation were examined by muscle biopsy and genetic screening. Both clinical and genetic features were analyzed. In all 40 cases with positive A3243G mutation, 36 children fitted clinical diagnosis of MELAS. In other 484 cases with negative mutation, only 8 children were clinically diagnosed with MELAS. Blood lactate levels in both groups were all elevated (P>0.05). In a further genetic screening of 28 families, 10 biological mothers and 8 silbings of MELAS children had positive A3243G point mutations but without any clinical symptoms. Certain difference existed in the clinical manifestations between children who were positive and negative for A3243G mutation of mtDNA but without statistical significance. MELAS showed maternal inheritance under most circumstances.     

家族性糖尿病人群中线粒体基因点突变的分析研究

目的 研究线粒体基因11个已知突变或变异在中国家族性糖尿病人群中的确切发生率及其与糖尿病的相关性.方法 应用聚合酶链反应一限制性片段长度多态结合直接测序方法 对随机抽取的无亲缘关系的770个糖尿病家系的先证者及309名非糖尿病对照者进行线粒体基因tRNALeu(3243,3256),tRNASer(12258),tRNAGlu(14709),tRNALys(8296,8344.8363),NDI(3316,3394,3426),ND4(12026)区11个已知位点突变或变异的筛查.结果 糖尿病先证者组中发现13例tRNALeu3243 A→G突变(1.69%),9例tRNAGlu14709 T→C变异(1.17%),17例ND1 3316 G→A变异(2.21%),18例ND13394 T→C变异(2.34%),28例ND412026 A→G变异(3.63%);在正常对照组中发现5例14709 T→C变异(1.62%),5例3316 G→A变异(1.62%)和6例3394 T→C变异(1.94%),9例12026 A→G变异(2.91%),未见到3243 A→G突变携带者.在两组中均未见到tRNALeu3256C→T,tRNALys 8296A→G,tRNALys8344A→G,tRNALys 8363G→A,tRNASer 12258C→A和ND1 3426 A→G突变.分别比较14709,3316,3394,12026位点变异在糖尿病先证者组和对照组的发生率以及临床资料,差异无统计学意义.在糖尿病先证者组中尚见到同时伴有两个位点改变的情况,其中3243 A→G突变和3394 T→C变异者2例,3243 A→G突变和12026 A→G变异2例.结论 线粒体基因tRNALeu(UUR) 3243 A→G突变是中国人线粒体糖尿病的主要致病基因,14709,3316,3394,12026位点变异可能是中国人线粒体基因多态,中国人群中未见到tRNALeu 3256C→T,tRNALys 8296A→G,tRNALys 8344A→G,tRNALys 8363G→A,tRNASer 12258C→A和ND1 3426 A→G突变,它们可能不是中国人线粒体糖尿病的致病基因.     

Nonrandom tissue distribution of mutant mtDNA.

Heteroplasmic mitochondrial DNA (mtDNA) defects are an important cause of inherited human disease. On a cellular level, the percentage of mutant mtDNA is the principal factor behind the expression of the genetic defect. Marked variation in the level of mutant mtDNA among tissues is thought to be responsible for the diverse clinical phenotypes associated with the same pathogenic mtDNA mutation. This study was designed to determine whether the percentage level of a pathogenic mtDNA molecule is determined by a purely random process. The tissue distribution of the A3243G MELAS point mutation was analyzed in five individuals who were members of a family with maternally inherited diabetes and deafness. The level of mutant mtDNA was measured in four tissues in three individuals and three tissues in two individuals. The highest level of mutant mtDNA occurred in skeletal muscle, followed by hair follicles, and then buccal mucosa, with the lowest levels in blood (leucocyte/platelet fraction). The probability of observing any strict hierarchy in family is 4.82 x 10(-5). These results indicate that the distribution of the A3243G mutation is not solely determined by random processes.     

Mutation screening of the mitochondrial genome using denaturing high-performance liquid chromatography

Over 170 known mutations of the mitochondrial genome are responsible for disease. Due to the unique features of mitochondrial genetics, such patients are clinically diverse and difficult to diagnose. As pathogenic mitochondrial DNA (mtDNA) mutations are mostly heteroplasmic, denaturing high-performance liquid chromatography (DHPLC) could be used to detect these heteroplasmic species and therefore act as a rapid screening test for mtDNA mutations. The entire mitochondrial genome was amplified by PCR in 40 overlapping regions. In addition, known mtDNA mutants were constructed for each of these regions using a PCR-based site-directed mutagenesis approach. These mutants were used as positive controls and showed a detection limit of 3-10% heteroplasmy by DHPLC (depending on the specific mutation) compared to 40% for conventional sequencing. To further validate the screening test, mtDNA from 17 patients with seven different pathogenic mutations was used to compare mutation detection by DHPLC and conventional sequencing. DHPLC had a sensitivity of 88% compared to 82% for sequencing. This increased to 100% sensitivity for DHPLC when excluding the m.8993T>G mutation. DHPLC analysis is therefore a sensitive, rapid and cost-effective method to screen for mutations in the mitochondrial genome. The role of pyrosequencing in the quantitation of mutant load for known mtDNA mutations was highlighted using the m.3243A>G mutation as an illustrative example. Pyrosequencing analysis was able to discriminate samples containing as little as 5% heteroplasmy and proved to be an accurate and reproducible method for estimation of mutant load.     

Nonrandom tissue distribution of mutant mtDNA

Heteroplasmic mitochondrial DNA (mtDNA) defects are an important cause of inherited human disease. On a cellular level, the percentage of mutant mtDNA is the principal factor behind the expression of the genetic defect. Marked variation in the level of mutant mtDNA among tissues is thought to be responsible for the diverse clinical phenotypes associated with the same pathogenic mtDNA mutation. This study was designed to determine whether the percentage level of a pathogenic mtDNA molecule is determined by a purely random process. The tissue distribution of the A3243G MELAS point mutation was analyzed in five individuals who were members of a family with maternally inherited diabetes and deafness. The level of mutant mtDNA was measured in four tissues in three individuals and three tissues in two individuals. The highest level of mutant mtDNA occurred in skeletal muscle, followed by hair follicles, and then buccal mucosa, with the lowest levels in blood (leucocyte/platelet fraction). The probability of observing any strict hierarchy in family is 4.82 × 10⁻⁵. These results indicate that the distribution of the A3243G mutation is not solely determined by random processes. Am. J. Med. Genet. 85:498–501, 1999. © 1999 Wiley-Liss, Inc.     

Differential occurrence of mutations in mitochondrial DNA of human skeletal muscle during aging

Seven mtDNA mutations (five base substitutions and two deletions) were studied in skeletal muscle samples of 18 human subjects aged 1 hr to 90 years. Quantitative PCR procedures were applied to determine the incidence (frequency of occurrence) and abundance (percentage of mutant mtDNA out of total mtDNA). The base substitutions, in general, showed a very early onset, three such mutations being detectable in the muscles of infants aged 1 hr and 5 weeks. Of two disease-associated point mutations studied, 3243 A→G showed significant accumulation with age (P < 0.05), while 8993 T→G showed no significant age accumulation (P > 0.1). Moreover, three arbitrarily chosen mutations (not disease-associated) showed no age-associated accumulation: two (7029 C→T and 7920 A→G) showed little change over the years (P > 0.1), while the other (13167 A→G) showed a significant decrease (P < 0.05). Both the 4,977-bp and 7,436-bp deletions showed a significant age-associated occurrence (P < 0.01 and P < 0.05, respectively). The age of onset of detectable deletions is about 20–40 years; thereafter, the incidence and abundance of deletions tend to increase as a function of advancing age. The seven specific mutations were found to occur independent of each other, indicating the random nature of mtDNA mutations in skeletal muscle. Moreover, the age-associated accumulation of multiple deletions was observed in the same set of muscle tissues, each extract displaying a unique set of multiple PCR products. Thus, mutations in mtDNA occur differentially in human skeletal muscle during aging. Hum Mutat 11:360–371, 1998. © 1998 Wiley-Liss, Inc.     

A novel heteroplasmic tRNAleu(CUN) mtDNA point mutation in a sporadic patient with mitochondrial encephalomyopathy segregates rapidly in skeletal muscle and suggests an approach to therapy

A novel mtDNA point mutation was detected in the tRNAleu(CUN) gene (G to A at position 12315) in a sporadic patient with chronic progressive external ophthalmoplegia, ptosis, limb weakness, sensorineural hearing loss and a pigmentary retinopathy. The mutation disrupts base pairing in the T psi C stem at a site which has been conserved throughout evolution. Although the other mtDNA tRNAleu gene (UUR) is a hotspot for mutation, this is the first pathogenic mutation to be reported in the gene coding for tRNAleu(CUN). MtDNAs carrying the mutation constituted 94% of total mtDNAs in two separate muscle biopsies. Single fibre analysis showed that skeletal muscle fibres without detectable cytochrome c oxidase activity (COX-ve fibres) contained predominantly mutant mtDNAs (93-98%) while fibres with apparently normal COX activity had up to 90% mutant mtDNAs, demonstrating that the G12315A mutation is functionally recessive. Immunofluorescence studies with specific antibodies to mtDNA- or nuclear-encoded subunits of COX were consistent with a defect in mitochondrial protein translation. The mutation was not present in blood cells or cultured fibroblasts and surprisingly, it could not be detected in satellite cells cultured from the patient's muscle. This pattern, which may by typical of patients who have inherited new germline pathogenic mtDNA mutations, possibly reflects loss of the mutation by random genetic drift in mitotic tissues and proliferation of mitochondria containing the mutant mtDNA in post- mitotic cells. The absence of mtDNA carrying the mutation in satellite cells suggests that regeneration of skeletal muscle fibres from satellite cells could restore a wild-type mtDNA genotype and normal muscle function.      

Two mtDNA mutations 14487T>C (M63V,ND6) and 12297T>C (tRNA Leu) in a Leigh syndrome family

Mitochondrial cytopathies are characterized by a large variability of clinical phenotypes and severity. The 14487T>C mutation in mtDNA has been recently described to be associated with Leigh syndrome. The 12297T>C mutation has been described in isolated dilated cardiomyopathy patients. Here, we report a family with multiple members who harbor both mutations, with only a few individuals who are affected with Leigh syndrome. Mitochondrial whole genome sequencing analysis in the proband’s muscle specimen detected two nearly homoplasmic mutations: 14487T>C (M63V in ND6) and 12297T>C in the tRNA ^Leu (CUN) gene. These two mutations were also detected in the blood, urine sediments, hair follicles, and buccal swab samples of all matrilineal relatives tested. All individuals tested were nearly homoplasmic for the 12297T>C mutation, but had variable degrees of heteroplasmy for 14487T>C. We also screened for the frequency of these two mutations. Of 268 patients with Leigh or Leigh-like disease, one case was found to harbor the 14487T>C mutation (0.3%), and one had the 12297T>C mutation (0.3%). Neither mutation was detected in the 88 patients meeting MELAS syndrome criteria nor in the 56 patients with respiratory chain complex I or I + III deficiency. In conclusion, the 14487T>C mutation appears as the primary etiology of Leigh syndrome in this family, demonstrating the high level of heteroplasmy needed for a clinically significant phenotype with this mutation. The 12297T>C mutation was not associated with dilated cardiomyopathy for the family members who were clinically evaluated and who were shown by testing to be nearly homoplasmic for that mutation.     

Independent occurrence of somatic mutations in mitochondrial DNA of human skin from subjects of various ages

The incidence (frequency of occurrence) and abundance (percentage of mutant out of total mtDNA population) of two different somatic mtDNA mutations in human skin were investigated in 44 subjects ranging from 19 to 87 years of age. Using quantitative allele-specific polymerase chain reaction (AS-PCR) to analyse the A→G base substitution at nucleotide 3243, 50% of the samples showed detectable levels of that particular mutation, with abundances ranging from 0.01% to 0.12%. In the same set of skin samples, the overall incidence of the 4977 bp “common” deletion was also ˜ 50%. Where detected, the abundance of this deletion ranged from 0.0002% to 0.1%. Comparative analyses of the incidence and abundance of these two mutations, collectively and in individual skin samples, led to these two conclusions: (1) there is independent occurrence of these two mtDNA mutations in human skin, and (2) whereas the 4977 bp deletion shows an age-associated accumulation in human skin, no age association is apparent for the 3243 A→G base substitution. Furthermore, in general, there is a much lower incidence of somatic mutations in mtDNA of human skin as compared to that in postmitotic tissues such as skeletal muscle. Hum Mutat 11:191–196, 1998. © 1998 Wiley-Liss, Inc.     

Molecular-clinical correlations in a family with variable tissue mitochondrial DNA T8993G mutant load

Unlike many pathogenic mitochondrial DNA mutations, the T8993G mutation associated with Leigh syndrome (LS) and neurogenic muscle weakness, ataxia, retinitis pigmentosa (NARP) typically shows little variation in mutant load between different tissue types. We describe the molecular and clinical findings in a family with variable disease severity and tissue T8993G mutant loads. Real-time ARMS qPCR testing showed that two brothers with features of NARP and LS had high mutant loads (>90%) in all tissues tested, similar to previously reported cases. Their sister, who has mild speech delay but attends normal school, was found to have a relatively high mutant load (mean 93%) in tissues derived from endoderm (buccal mucosa) and mesoderm (blood and skin fibroblasts). However, in tissue derived from ectoderm (hair bulbs), she carried a considerably lower proportion of mutant mtDNA. Because both surface ectoderm, which gives rise to outer epithelia and hair, and neuroectoderm, which gives rise to the central nervous system, are derived from ectoderm, it is tempting to speculate that the mutant load detected in the oligosymptomatic sister's hair bulbs is a reflection of the brain mutant load. We conclude that significant variation in tissue mutant load may occur in at least some individuals that harbor the T8993G mutation. This adds additional complexity to genetic counseling and prenatal diagnosis in such instances. Given the shared embryonic origin of hair bulbs and brain, we recommend performing hair bulb mtDNA analysis in asymptomatic or oligosymptomatic individuals that have high blood mutant loads in order to understand better the genotype-phenotype correlations related to the T8993G mutation.     

运城地区耳聋患者常见耳聋基因突变分析

目的通过筛查运城地区耳聋患者常见耳聋基因GJB2、PDS和线粒体DNAl555位点的突变频率,来研究该地区常见耳聋基因突变的发生情况。方法采集运城市特殊教育学校75例耳聋患者外周血,对目的基因扩增并测序。结果75例患者中,45例患者的GJB2基因发生突变,其中,c．235delc、e．79G〉A和c.341A〉G的突变频率较高,分别为12％、22％和18．7％,另外还检测出4个突变频率较低的位点C．608T〉C（2％）、C．109G〉A（0．67％）、c．368C〉A（1．33％）和C．176—191del16（0．67％）;3例患者的PDS基因第19外显子发生突变,C．2168A〉G与IVs7—2G〉A突变频率分别为1．33％和2％;仅有1例患者mtDNA1555发生突变。结论通过对山西运城地区常见耳聋基因突变的研究,对建立山西省耳聋基因突变数据库提供素材,同时也为耳聋的预防,基因诊断及治疗提供强有力的依据。     

A patient with two mitochondrial DNA mutations causing PEO and LHON

We report a 22-year-old man with PEO and optic atrophy. PEO developed before the onset of optic atrophy. The patient showed mitochondrial myopathy with cytochrome c oxidase deficient fibers.In skeletal muscle the patient was homoplasmic for the mtDNA G11778A Leber hereditary optic neuropathy (LHON) mutation and heteroplasmic for the mtDNA 5 kb “common” deletion mutation. In blood only the homoplasmic LHON mutation was identified.The occurrence of two pathogenic mtDNA mutations is exceedingly rare. The clinical findings in this patient indicate that the combination of the two mtDNA mutations resulted in the expected combined phenotype since the mtDNA deletion mutation accounted for the PEO and the mtDNA G11778A point mutation for the optic atrophy.     

大同地区耳聋基因GJB2和mtDNA1555突变分析

目的通过筛查大同地区87例耳聋患者常见基因GJB2和mtDNA1555的突变频率,研究该地区CJB2和mtD-NA1555基因突变情况及热点突变位点。方法采集大同地区87例耳聋患者外周血,对目的基因扩增并进行测序分析。结果所有患者中有58例GJB2基因检测到11个突变位点,与编码连接蛋白的非综合征耳聋突变数据库（http：／／davinci．crg．es／deafness／index．php？section=mut_db＆db=nonsynd）比对,9个位点已见报道,其中包括5个多肽位点c．79G〉A、c．341A〉G、c．608T〉C、c．368C〉A、c．765T〉C和4个致病住点c．235delc、c．109G〉A、c．176-c．191del16和c．299-c．300delAT,其中,c．79G〉A是主要突变方式,携带率为24．14％（42／174）。新发现两例未见报道的突变位点c．277A〉G和c．558G〉A;患者中只有1例检测到mtDNA1555A〉G位点突变。结论通过对大同地区GJB2基因和mtD-NA1555突变位点的研究,了解大同地区该基因突变谱,为后续国内耳聋基因型分布提供数据支持,同时也为耳聋的早期诊断,治疗提供理论依据。     

早发糖尿病线粒体基因突变的研究

目的研究天津地区早发糖尿病(发病年龄≤45岁)中线粒体基因突变的发生率及其相关性。方法随机选取无血缘关系、发病年龄≤45岁的糖尿病患者348例;对照组207名,收集相应临床资料,提取外周血基因组DNA,应用聚合酶链反应-限制性片段长度多态性及克隆技术检测线粒体基因点突变。结果糖尿病组线粒体基因点突变总的发生率为8.3%,明显高于对照组(3.3%)(P<0.05),其中17例ND412026A→G突变(4.9%);10例ND1点突变(2.9%),其中包括4例3316G→A突变(1.2%),5例3394T→C突变(1.4%),1例3426A→G突变(0.3%);2例3243A→G突变,检出率为0.6%。在对照组中发现4例12026A→G(1.9%);2例3394T→C突变(0.9%);1例G3316G→A突变(0.5%);未发现3243A→G突变和3426A→G突变。结论天津地区早发糖尿病患者存在多种线粒体基因点突变。     

Clinical heterogeneity in mitochondrial DNA deletion disorders: a diagnostic challenge of Pearson syndrome

The clinical presentation of mitochondrial DNA (mtDNA) disorders is quite diverse. Very often, the initial symptoms do not fit a specific disease, and diagnosis is difficult to make. We describe a patient who presented with macrocytic anemia. Extensive biochemical and clinical work-up failed to provide an etiology for the macrocytic anemia. The patient over the course of 6 years developed gait problems, exercise intolerance, episodic vomiting, short stature, dermatological problems, and recurrent infection. At age 8 years she had encephalopathy with ataxia and dysphagia. The presence of elevated lactate, bilateral basal ganglia calcification, and ragged red fibers led to mtDNA mutational analysis. A novel 4.4-kb deletion from nucleotide position 10,560 to nucleotide position 14, 980 was identified in muscle biopsy. The same heteroplasmic mtDNA deletion was present in blood, buccal cells, and hair follicles, but not in mother's blood, consistent with sporadic mutation in the patient. This case emphasizes the importance of considering mtDNA disorder in patients with multisystemic symptoms that cannot be explained by a specific diagnosis.     

Quantitative allele-specific PCR: Demonstration of age-associated accumulation in human tissues of the A→G mutation at nucleotide 3243 in mitochondrial DNA

We have developed an improved allele-specific polymerase chain reaction (AS-PCR) procedure that can selectively amplify mutant DNA sequences (which differ from the normal sequences by a single base pair) in the presence of large excess of normal sequences. We applied this procedure to quantification of mutant molecules of human mitochondrial DNA (mtDNA). Conditions for AS-PCR have been systematically varied, encompassing DNA template input, annealing temperature, and PCR cycle number. Adjustment of these three reaction parameters to optimal conditions, using plasmids containing cloned segments of mutant and normal mtDNA, enabled the reliable detection of as little as 0.01% of mutant mtDNA. By standardising the DNA input for AS-PCR, the percentage of mutant molecules can be accurately quantified. This improved procedure was used here to detect and quantify the base substitution at nucleotide position 3243 (A→G) in mtDNA from total cellular DNA isolated from various tissues of both infants and adults. We observed a 5- to 10-fold higher mutant mtDNA (3243 A→G) frequency in adult tissues than in infant tissues. The results are consistent with the hypothesis that the accumulation of mtDNA mutations is an important feature of the human aging process. The quantitative and sensitive allele-specific amplification system described here is applicable to the quantification of low levels of somatic mutations in oncogenes and tumour suppressor genes in the context of human mutation, and could be extended to any biological situation in which only a small proportion of a DNA molecular population is subjected to a particular base substitution. Hum Mutat 9: 265–271, 1997. © 1997 Wiley-Liss, Inc.     

Chip-based mtDNA mutation screening enables fast and reliable genetic diagnosis of OXPHOS patients.

PURPOSE: Oxidative phosphorylation is under dual genetic control of the nuclear and the mitochondrial DNA (mtDNA). Oxidative phosphorylation disorders are clinically and genetically heterogeneous, which makes it difficult to determine the genetic defect, and symptom-based protocols which link clinical symptoms directly to a specific gene or mtDNA mutation are falling short. Moreover, approximately 25% of the pediatric patients with oxidative phosphorylation disorders is estimated to have mutations in the mtDNA and a standard screening approach for common mutations and deletions will only explain part of these cases. Therefore, we tested a new CHIP-based screening method for the mtDNA. METHODS: MitoChip (Affymetrix) resequencing was performed on three test samples and on 28 patient samples. RESULTS: Call rates were 94% on average and heteroplasmy detection levels varied from 5-50%. A genetic diagnosis can be made in almost one-quarter of the patients at a potential output of 8 complete mtDNA sequences every 4 days. Moreover, a number of potentially pathogenic unclassified variants (UV) were detected. CONCLUSIONS: The availability of long-range PCR protocols and the predominance of single nucleotide substitutions in the mtDNA make the resequencing CHIP a very fast and reliable method to screen the complete mtDNA for mutations.