Nuclear DNA analysis

Laboratory tests

Single gene analysis: The RCMM offers DNA diagnostics for nuclear encoded subunits and assembly factors of the respiratory chain enzymes (complex I, II, III, and IV), the F1F0-type ATPase (complex V), pyruvate dehydrogenase and pyruvate carboxylase. In addition, a large number of additional genes associated with mitochondrial disease is offered, including genes involved in mitochondrial translation, mtDNA depletion and mitochondrial fission/fusion. In total more than 100 nuclear encoded genes involved in the mitochondrial energy generating system can be investigated. MLPA tests are available for a limited number of genes, including POLG.

Whole exome sequencing: In addition to sequencing of individual genes, whole exome sequencing is offered as a diagnostic test for mitochondrial disease. The analysis is performed in two steps. First, a package of more than 250 genes known to be associated with mitochondrial disease is examined and results are reported. If negative, the complete exome is examined for mutations in genes not previously known to be associated with mitochondrial disease. All variants that are identified by exome sequencing are validated by Sanger sequencing. For details please contact us. For mitochondrial DNA analysis please see under the specific heading on this website.

Shipping and Handling samples

For nDNA diagnostics a blood sample (5-10 ml) collected in plastic EDTA-tubes is required. The sample can be sent to the RCMM by regular mail at room temperature. For long distance shipment we advise to use courier service. For complex diagnostic questions please contact us before sending samples. For DNA diagnostics at the RNA level heparin blood (at least 10 ml) has to be collected in plastic tubes. Please send the sample on ice within 24 hours by express post to our center. In case fibroblast cell lines are available we prefer to receive these for the analyses on RNA level. In that case, genetic tests can be combined with enzyme testing (see “Biochemistry” on this website). For prenatal diagnostics, please contact us before sending the material. For prenatal diagnostics 30 mg chorionic villi have to be collected as well as EDTA blood (plastic tube) of the mother for maternal contamination testing. Postnatal DNA diagnostics will be completed within 6 to 8 weeks after receipt of the sample. Reporting time of whole exome sequencing, including clinical validation, is 4-6 months. A report of the prenatal diagnosis will be ready within 1 to 2 weeks.

Diagnostic request forms

Please use the forms when sending us samples for diagnostic analysis.

Billing

In accordance with the Dutch regulations for DNA diagnostics. For details please contact our secretary (see contact options on main research page).

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Centers of clinical expertise Centers of clinical expertise Inherited Metabolic Disease Specialized diagnostics

Specialized diagnostics

Our diagnostics of mitochondrial disorders is performed at the levels of biochemistry, mitochondrial DNA analysis, nuclear DNA analysis, pathology, and prenatal diagnostics.

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General services

Each year, the RCMM receives samples of patients from all over the world for diagnostic analysis of mitochondrial disorders. We offer biochemical, histological and genetic analysis of frozen tissue samples, cultured skin fibroblasts and blood/DNA samples. For hospitals located within a two hour travel time from Nijmegen, biochemical analysis of fresh muscle samples is offered as well. In addition, we perform biochemical and genetic tests for prenatal diagnostics of mitochondrial disorders.

Specific services

  • We examine more than 600 patient samples each year.

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    Biochemistry

    General information

    In 1975, our laboratory started research and diagnostics of mitochondrial myopathies with 3 employees. Nowadays, we examine more than 600 patient samples each year. The experience and knowledge about functioning and disfunctioning of mitochondria in health and disease that we have build up in the past decades is applied to the diagnostic analysis of new patients in our center every day.

    Laboratory tests

    The biochemical laboratory offers a broad diagnostic package for the functional analysis of the mitochondrial energy generating system in different types of tissue samples and cultured cells. Analysis of a fresh muscle biopsy is regarded to be the gold standard in the diagnostics of mitochondrial disorders. In a freshly collected muscle sample, the overall activity of the mitochondrial ATP generating system is evaluated by measurements of oxidation rates of several 14C-labelled substrates, and production of ATP from the oxidation of pyruvate + malate. In addition, activities of single enzymes from the respiratory chain (complex I, II, III, and IV), ATPase/complex V and pyruvate dehydrogenase (PDHc) are measured in fresh muscle biopsies. In frozen muscle biopsies (and biopsies from other tissues) complex I, II, III, and IV, as well as PDHc can be measured. In fibroblasts both the overall capacity of the energy generating system and single enzymes (complex I, II, III, IV, V, PDHc, pyruvate carboxylase) can be measured. In both muscle and fibroblasts, coenzyme Q10 can be measured by HPLC-ECD. Should the diagnostic results give cause for this, several additional laboratory tests are available that are performed on research base. In certain cases we can also offer prenatal diagnostics at the enzyme level for PDHc, complex l, complex lV, and complex V.

    Recently we have set up a functional genomics facility for the analysis of the functional implications of new sequence variations (obtained by Sangers sequencing, whole exome sequencing or whole genome sequencing) in genes encoding proteins involved in the mitochondrial energy generating system. For more information, please inquire.

    Reporting of results

    A written report concerning the biochemical studies performed in skeletal muscle will be supplied within 6 to 8 weeks. Depending on the growth characteristics of the cells, results of fibroblast biochemical analysis will be reported within 3 months.

    Diagnostic request forms

    Please use the forms when sending us samples for diagnostic analysis.

    Billing

    In accordance with the Dutch regulations for enzyme diagnostics. For details please contact our secretary (see contact options on main research page).

  • Mitochondrial DNA analysis

    Laboratory tests

    We offer complete sequence analysis of the mtDNA using an Iontorrent platform. Before sequencing, the mtDNA is routinely tested for the presence of deletions and rearrangements. In the case of a clinically distinct presentation associated with mtDNA single nucleotide mutations (e.g. the MELAS/MIDD m.3243A>G mutation), pyrosequencing can be performed to determine heteroplasmy levels. In case of a suspected mtDNA depletion syndrome, we offer a QPCR-based test to quantify mtDNA content in muscle tissue. Because of tissue-specific heteroplasmy levels, analysis of clinically and/or biochemically (e.g. enzyme deficiency) affected tissue is usually preferred. The mtDNA analysis can be combined with biochemical testing (see under “Biochemistry” on this website). Biopsy material (muscle, skin, etc) for the purpose of DNA analysis should be sent deeply frozen. For the analysis of the m.3243A>G mutation, a urine sample can be send in. For analysis of LHON mutations and for suspected Pearson syndrome, an EDTA blood sample can be send in. For all other mtDNA tests, muscle is preferred. For more information please contact us. Reporting time is 6 to 8 weeks after receipt of the sample.

    Diagnostic request forms

    Please use the forms when sending us samples for diagnostic analysis.

    Billing

    Billing is in accordance with the Dutch regulations for DNA diagnostics. For details please contact our secretary (see contact options on main research page).

  • Pathology

    Laboratory tests

    Routinely enzymehistochemical and morphometric examination is performed on frozen muscle samples. The following stains are routinely performed: HE, Gomori trichrome , Sudan Black, PAS, acid phosphatase, ATPase at pH 4.2, 4.6 and 10.3, NADH, SDH and COX. Based on the initial findings the examination is completed with immunohistochemistry and electron microscopy.

    Shipping and Handling

    The material for enzyme and immunohistochemistry must be snap frozen in isopentane -140 Celcius chilled in liquid nitrogen. When frozen this way it can be sent on dry ice. For electron microscopy fixation in 2% buffered glutaraldehyde is necessary.

    Reporting of results

    A preliminary report is available at the day following the biopsy. A final report is sent out as soon as all the test results have been obtained. This is routinely within 3 weeks from the date of receipt of the request form with material.

    Billing

    In accordance with Dutch regulations the costs are 89 Euro for histopathological examination, 357 Euro for enzymehistochemical examination, 176 Euro for morphometric examination, 357 Euro for immunohistochemical examination and 375 Euro for electron microscopy.

  • Prenatal diagnostics

    When can we offer prenatal diagnostics

    The bi-genomic (mtDNA as well as nDNA) nature of the oxidative phosphorylation system makes genetic counseling and prenatal diagnosis a difficult enterprise. Enzyme complex OXPHOS-system deficiencies may be caused by mtDNA or nDNA mutations. Consequently the inheritance of this group of mitochondrial energy production disturbances is either maternal or Mendelian.

    We can offer prenatal diagnosis if:

    • The causative nuclear mutation in a family is known, or
    • The enzyme complex deficiency has been established in two different tissues, among obligatory cultured skin fibroblasts.

    The most experience with prenatal diagnosis we have for isolated complex I and IV deficiencies. This has among others to do with the relatively high frequency of both enzyme complex deficiencies.

    More information

    For more information regarding precautions and procedures please feel free to contact us (see contact options on main research page).