• diseases
• medical genetics
• molecular medicine

• Humans
• Mitochondrial Diseases/genetics
• Mitochondrial Diseases/therapy
• Mitochondrial Diseases/metabolism
• Mitochondrial Diseases/pathology
• Mitochondria/genetics
• Mitochondria/metabolism
• Mitochondria/pathology
• Oxidative Phosphorylation
• DNA, Mitochondrial/genetics
• Mutation
• Mitochondrial Proteins/genetics
• Mitochondrial Proteins/metabolism

• 82271110 National Natural Science Foundation of China (National Science Foundation of China)
• New Technology Incubation Funds in Ophthalmology
• Undergraduate Training Program for Innovation and Entrepreneurship of Hunan Province (No. S202410533161)

• Inherited retinal degeneration
• Peroxisomal disorders
• Retina
• Retinitis pigmentosa
• Rod-cone dystrophy
• Syndrome

• Analytical methods
• Heteroplasmy
• Mitochondrial DNA
• Preimplantation genetic diagnosis
• Prenatal diagnosis

• Female
• Humans
• Pregnancy
• DNA, Mitochondrial/genetics
• Mitochondria/genetics
• Mutation/genetics
• Polymerase Chain Reaction
• Preimplantation Diagnosis
• High-Throughput Nucleotide Sequencing/methods
• Sequence Analysis, DNA/methods

• 2021YFC2700901 National Key R&D Program of China
• 82001635 National Natural Science Foundation of China
• 81971455 National Natural Science Foundation of China
• U20A20350 National Natural Science Foundation of China
• 202204295107020012 Clinical Medical research transformation Project of Anhui Province
• 2022LCX015 Foundation for Selected Scientists Studying Abroad of Anhui Province
• gxyqZD2022027 Program for Outstanding Young Talents in University of Anhui
• National Key R&D Program of China
• Program for Outstanding Young Talents in University of Anhui

• disease genetics
• hereditary eye disease

• Wellcome Trust
• SAC051 National Eye Research Centre (NERC)
• 206619/Z/17/Z Wellcome Trust (Wellcome)
• 5045/46 Fight for Sight UK

• NGS
• OXPHOS
• mitochondrial disorder
• mtDNA
• nDNA

• population genetics
• genomics
• next-generation sequencing

• Benchmarking
• Computational Biology/methods
• DNA, Mitochondrial/classification
• Genome, Mitochondrial
• Haplotypes
• Humans
• Whole Genome Sequencing

• Ministerio de Educación y Formación Profesional, España

• congenital anomalies
• genetics
• infant mortality
• morphogenesis
• phenotype
• risk assessment

Mitochondrial Cardiomyopathy (MCM) is a common manifestation of multi-organ Mitochondrial Diseases (MDs), occasionally present in non-syndromic cases. Diagnosis of MCM is complex because of wide clinical and genetic heterogeneity and requires medical, laboratory, and neuroimaging investigations. Currently, the molecular screening for MCM is fundamental part of MDs management and allows achieving the definitive diagnosis. In this article, we review the current genetic knowledge associated with MDs, focusing on diagnosis of MCM and MDs showing cardiac involvement. We searched for publications on mitochondrial and nuclear genes involved in MCM, mainly focusing on genetic screening based on targeted gene panels for the molecular diagnosis of the MCM, by using Next Generation Sequencing. Here we report twelve case reports, four case-control studies, eleven retrospective studies, and two prospective studies, for a total of twenty-nine papers concerning the evaluation of cardiac manifestations in mitochondrial diseases. From the analysis of published causal mutations, we identified 130 genes to be associated with mitochondrial heart diseases. A large proportion of these genes (34.3%) encode for key proteins involved in the oxidative phosphorylation system (OXPHOS), either as directly OXPHOS subunits (22.8%), and as OXPHOS assembly factors (11.5%). Mutations in several mitochondrial tRNA genes have been also reported in multi-organ or isolated MCM (15.3%). This review highlights the main disease-genes, identified by extensive genetic analysis, which could be included as target genes in next generation panels for the molecular diagnosis of patients with clinical suspect of mitochondrial cardiomyopathies.

• diagnosis
• genetic testing
• mitochondrial DNA
• mitochondrial cardiomyopathy
• mitochondrial disease
• mutation
• next generation sequencing

• Alleles
• Cardiomyopathies/diagnosis
• Cardiomyopathies/epidemiology
• Cardiomyopathies/etiology
• Disease Susceptibility
• Genes, Mitochondrial
• Genetic Predisposition to Disease
• Genetic Testing
• Humans
• Mitochondria/genetics
• Mitochondria/metabolism
• Mitochondrial Diseases/diagnosis
• Mitochondrial Diseases/epidemiology
• Mitochondrial Diseases/etiology
• Molecular Epidemiology
• Mutation
• Organ Specificity
• Phenotype

Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of “unknown significance” can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain “not genetically defined”. In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss “facilitations and hurdles” of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of “therapeutic offer”.

• genetic testing
• neuromuscular disease
• next generation sequencing
• whole exome sequencing

• genetic testing
• neuromuscular disease
• next generation sequencing
• whole exome sequencing

• diagnostics
• genetics
• metabolic disorders
• mitochondrial disease
• multiomics
• noncoding
• oxidative phosphorylation
• variants

• clinical diagnostics
• gene panel
• mitochondria
• next generation sequencing

• inherited rare disease
• precise clinical diagnosis
• syndromic retinal disease
• whole-exome sequencing

• Adult
• Carboxypeptidases/genetics
• Carboxypeptidases/metabolism
• DNA/genetics
• DNA Mutational Analysis
• Electrooculography
• Electroretinography
• Exome
• Female
• Homozygote
• Humans
• Male
• Mutation
• Pedigree
• Retina/pathology
• Retinal Dystrophies/diagnosis
• Retinal Dystrophies/genetics
• Tomography, Optical Coherence
• Exome Sequencing/methods
• Young Adult

• ZIA EY000546 Intramural NIH HHS
• #300009177 to SK Chief Scientist Office of the Israeli Ministry of Health and the Lirot association
• BR-GE-0214-0639 to DS and EB Foundation Fighting Blindness
• #2154/15 to SK Israel Science Foundation

• ES data
• bioinformatics
• mtDNA
• pipeline

• Leber hereditary optic neuropathy
• next-generation sequencing
• whole genome sequencing

Since the advent of next generation sequencing (NGS), several studies have tried to evaluate the relevance of targeted gene panel sequencing and whole exome sequencing for molecular diagnosis of mitochondrial diseases. The comparison between these different strategies is extremely difficult. A recent study analysed a cohort of patients affected by a mitochondrial disease using a NGS approach based on a targeted gene panel including 132 genes. This strategy led to identify the causative mutations in 15.2% of cases. The number of novel genes responsible for respiratory chain deficiency increases very rapidly.

In order to determine the impact of larger panels used as a first screening strategy on molecular diagnosis success, we analysed a cohort of 80 patients affected by a mitochondrial disease with a first mitochondrial DNA (mtDNA) NGS screening and secondarily a targeted mitochondrial panel of 281 nuclear genes.

Pathogenic mtDNA abnormalities were identified in 4.1% (1/24) of children and 25% (14/56) of adult patients. The remaining 65 patients were analysed with our targeted mitochondrial panel and this approach enabled us to achieve an identification rate of 21.7% (5/23) in children versus 7.1% (3/42) in adults.

Our results confirm that larger gene panels do not improve diagnostic yield of mitochondrial diseases due to (i) their very high genetic heterogeneity, (ii) the ongoing discovery of novel genes and (iii) mutations in genes apparently not related to mitochondrial function that lead to secondary respiratory chain deficiency.

The online version of this article (10.1186/s12881-018-0568-y) contains supplementary material, which is available to authorized users.

• Exome
• Mitochondrial disorders
• Next generation sequencing
• Targeted panel

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.

• heteroplasmy
• mitochondria
• mtDNA
• next generation sequencing

• clinical features
• gene
• mitochondrial disease
• targeted next generation sequencing

Whole-exome sequencing (WES) has led to an exponential increase in identification of causative variants in mitochondrial disorders (MD).

We performed WES in 113 MD suspected patients from Polish paediatric reference centre, in whom routine testing failed to identify a molecular defect. WES was performed using TruSeqExome enrichment, followed by variant prioritization, validation by Sanger sequencing, and segregation with the disease phenotype in the family.

Likely causative mutations were identified in 67 (59.3 %) patients; these included variants in mtDNA (6 patients) and nDNA: X-linked (9 patients), autosomal dominant (5 patients), and autosomal recessive (47 patients, 11 homozygotes). Novel variants accounted for 50.5 % (50/99) of all detected changes. In 47 patients, changes in 31 MD-related genes (ACAD9, ADCK3, AIFM1, CLPB, COX10, DLD, EARS2, FBXL4, MTATP6, MTFMT, MTND1, MTND3, MTND5, NAXE, NDUFS6, NDUFS7, NDUFV1, OPA1, PARS2, PC, PDHA1, POLG, RARS2, RRM2B, SCO2, SERAC1, SLC19A3, SLC25A12, TAZ, TMEM126B, VARS2) were identified. The ACAD9, CLPB, FBXL4, PDHA1 genes recurred more than twice suggesting higher general/ethnic prevalence. In 19 cases, variants in 18 non-MD related genes (ADAR, CACNA1A, CDKL5, CLN3, CPS1, DMD, DYSF, GBE1, GFAP, HSD17B4, MECP2, MYBPC3, PEX5, PGAP2, PIGN, PRF1, SBDS, SCN2A) were found. The percentage of positive WES results rose gradually with increasing probability of MD according to the Mitochondrial Disease Criteria (MDC) scale (from 36 to 90 % for low and high probability, respectively). The percentage of detected MD-related genes compared with non MD-related genes also grew with the increasing MD likelihood (from 20 to 97 %). Molecular diagnosis was established in 30/47 (63.8 %) neonates and in 17/28 (60.7 %) patients with basal ganglia involvement. Mutations in CLPB, SERAC1, TAZ genes were identified in neonates with 3-methylglutaconic aciduria (3-MGA) as a discriminative feature. New MD-related candidate gene (NDUFB8) is under verification.

We suggest WES rather than targeted NGS as the method of choice in diagnostics of MD in children, including neonates with 3-MGA aciduria, who died without determination of disease cause and with limited availability of laboratory data. There is a strong correlation between the degree of MD diagnosis by WES and MD likelihood expressed by the MDC scale.

The online version of this article (doi:10.1186/s12967-016-0930-9) contains supplementary material, which is available to authorized users.

• 3-methylglutaconic aciduria
• Basal ganglia involvement
• Candidate gene
• Leigh syndrome
• Mitochondrial disease criteria scale
• Mitochondrial disorders
• Neonates
• Novel mutation
• Whole-exome sequencing

We previously described increased levels of growth and differentiation factor 15 (GDF-15) in skeletal muscle and serum of patients with mitochondrial diseases. Here we evaluated GDF-15 as a biomarker for mitochondrial diseases affecting children and compared it to fibroblast-growth factor 21 (FGF-21). To investigate the mechanism of GDF-15 induction in these pathologies we measured its expression and secretion in response to mitochondrial dysfunction.

We analysed 59 serum samples from 48 children with mitochondrial disease, 19 samples from children with other neuromuscular diseases and 33 samples from aged-matched healthy children. GDF-15 and FGF-21 circulating levels were determined by ELISA.

Our results showed that in children with mitochondrial diseases GDF-15 levels were on average increased by 11-fold (mean 4046pg/ml, 1492 SEM) relative to healthy (350, 21) and myopathic (350, 32) controls. The area under the curve for the receiver-operating-characteristic curve for GDF-15 was 0.82 indicating that it has a good discriminatory power. The overall sensitivity and specificity of GDF-15 for a cut-off value of 550pg/mL was 67.8% (54.4%-79.4%) and 92.3% (81.5%-97.9%), respectively. We found that elevated levels of GDF-15 and or FGF-21 correctly identified a larger proportion of patients than elevated levels of GDF-15 or FGF-21 alone. GDF-15, as well as FGF-21, mRNA expression and protein secretion, were significantly induced after treatment of myotubes with oligomycin and that levels of expression of both factors significantly correlated.

Our data indicate that GDF-15 is a valuable serum quantitative biomarker for the diagnosis of mitochondrial diseases in children and that measurement of both GDF-15 and FGF-21 improves the disease detection ability of either factor separately. Finally, we demonstrate for the first time that GDF-15 is produced by skeletal muscle cells in response to mitochondrial dysfunction and that its levels correlate in vitro with FGF-21 levels.

• Adolescent
• Animals
• Biomarkers/blood
• Case-Control Studies
• Cell Line
• Child
• Child, Preschool
• Cohort Studies
• Female
• Fibroblast Growth Factors/blood
• Growth Differentiation Factor 15/blood
• Humans
• Infant
• Male
• Mice
• Mitochondrial Diseases/blood
• Muscle Fibers, Skeletal/metabolism
• Muscle, Skeletal/metabolism
• Myoblasts/metabolism
• Neuromuscular Diseases/blood
• RNA, Messenger/metabolism
• ROC Curve
• Reproducibility of Results
• Sensitivity and Specificity

• MTFMT
• children
• mitochondrial translation
• neuroimaging
• neuromyelitis optica

• Adenine Nucleotide Translocator 1/genetics
• Adolescent
• Animals
• Female
• Humans
• Male
• Mitochondrial Myopathies/genetics
• Models, Animal
• Mutation
• Pedigree
• RNA, Messenger/genetics
• Zebrafish

• K01 AR062601 NIAMS NIH HHS
• T32 GM008283 NIGMS NIH HHS
• P30 HD018655 NICHD NIH HHS
• P30-HD-18655 NICHD NIH HHS
• F31 NS081928 NINDS NIH HHS

• Clinical genetics
• Diagnostics tests
• Haematology (incl Blood transfusion)
• Other oncology

• Alpers syndrome
• CARS2
• aminoacyl-tRNA synthetases
• exome sequencing
• mitochondrial translation

• Copy number
• Heteroplasmy
• High throughput sequencing
• Mutation
• Next generation sequencing
• SNP

• DNA Copy Number Variations
• DNA, Mitochondrial/chemistry
• DNA, Mitochondrial/genetics
• Genetic Variation
• High-Throughput Nucleotide Sequencing/methods
• High-Throughput Nucleotide Sequencing/statistics & numerical data
• Humans
• Mitochondrial Diseases/diagnosis
• Polymorphism, Single Nucleotide

• P30 CA068485 NCI NIH HHS

Mitochondrial dysfunction accounts for a large group of inherited metabolic disorders most of which are due to a dysfunctional mitochondrial respiratory chain (MRC) and, consequently, deficient energy production. MRC function depends on the coordinated expression of both nuclear (nDNA) and mitochondrial (mtDNA) genomes. Thus, mitochondrial diseases can be caused by genetic defects in either the mitochondrial or the nuclear genome, or in the cross-talk between the two. This impaired cross-talk gives rise to so-called nuclear-mitochondrial intergenomic communication disorders, which result in loss or instability of the mitochondrial genome and, in turn, impaired maintenance of qualitative and quantitative mtDNA integrity. In children, most MRC disorders are associated with nuclear gene defects rather than alterations in the mtDNA itself.

The mitochondrial DNA depletion syndromes (MDSs) are a clinically heterogeneous group of disorders with an autosomal recessive pattern of transmission that have onset in infancy or early childhood and are characterized by a reduced number of copies of mtDNA in affected tissues and organs. The MDSs can be divided into least four clinical presentations: hepatocerebral, myopathic, encephalomyopathic and neurogastrointestinal. The focus of this review is to offer an overview of these syndromes, listing the clinical phenotypes, together with their relative frequency, mutational spectrum, and possible insights for improving diagnostic strategies.

• Full mitochondrial genome
• Molecular divergence
• Next Generation Sequencing
• Phylogenetics

• Hippocampal sclerosis
• MT-ATP8
• MT-ND4
• MT-ND5
• Mesial temporal lobe epilepsy

Intervertebral disc (IVD) cells experience a broad range of physicochemical stimuli under physiologic conditions, including alterations in their osmotic environment. At present, the molecular mechanisms underlying osmotic regulation in IVD cells are poorly understood. This study aims to screen genes affected by changes in osmotic pressure in cells of subjects aged 29 to 63 years old, with top-scoring pair (TSP) method.

Gene expression data set GSE1648 was downloaded from Gene Expression Omnibus database, including four hyper-osmotic stimuli samples, four iso-osmotic stimuli samples, and three hypo-osmotic stimuli samples. A novel, simple method, referred to as the TSP, was used in this study. Through this method, there was no need to perform data normalization and transformation before data analysis.

A total of five pairs of genes ((CYP2A6, FNTB), (PRPF8, TARDBP), (RPS5, OAZ1), (SLC25A3, NPM1) and (CBX3, SRSF9)) were selected based on the TSP method. We inferred that all these genes might play important roles in response to osmotic stimuli and age in IVD cells. Additionally, hyper-osmotic and iso-osmotic stimuli conditions were adverse factors for IVD cells.

We anticipate that our results will provide new thoughts and methods for the study of IVD disease.

Mitochondrial disorders are difficult to diagnose due to extreme genetic and phenotypic heterogeneities.

We explored the utility of targeted next-generation sequencing for the diagnosis of mitochondrial disorders in 148 patients submitted for clinical testing. A panel of 447 nuclear genes encoding mitochondrial respiratory chain complexes, and other genes inducing secondary mitochondrial dysfunction or that cause diseases which mimic mitochondrial disorders were tested.

We identified variants considered to be possibly disease-causing based on family segregation data and/or variants already known to cause disease in twelve genes in thirteen patients. Rare or novel variants of unknown significance were identified in 45 additional genes for various metabolic, genetic or neurogenetic disorders.

Primary mitochondrial defects were confirmed only in four patients indicating that majority of patients with suspected mitochondrial disorders are presumably not the result of direct impairment of energy production. Our results support that clinical and routine laboratory ascertainment for mitochondrial disorders are challenging due to significant overlapping non-specific clinical symptoms and lack of specific biomarkers. While next-generation sequencing shows promise for diagnosing suspected mitochondrial disorders, the challenges remain as the underlying genetic heterogeneity may be greater than suspected and it is further confounded by the similarity of symptoms with other conditions as we report here.

• biocontrol
• fertility control
• mathematical model
• mtDNA
• population viability
• sterile male technique

Differences between genomes can be due to single nucleotide variants, translocations, inversions, and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 500 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease. Hence there is a need for better-tailored and more robust tools for the detection and genome-wide analyses of CNVs. While a link between a given CNV and a disease may have often been established, the relative CNV contribution to disease progression and impact on drug response is not necessarily understood. In this review we discuss the progress, challenges, and limitations that occur at different stages of CNV analysis from the detection (using DNA microarrays and next-generation sequencing) and identification of recurrent CNVs to the association with phenotypes. We emphasize the importance of germline CNVs and propose strategies to aid clinicians to better interpret structural variations and assess their clinical implications.

• bioinformatics
• complex disease
• copy number variation
• genome-wide association studies
• genomics
• personalized medicine
• sequencing