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Autosomal Dominant Progressive External Ophthalmoplegia and other C10orf2-related disorders via the TWNK/C10orf2 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1255 TWNK$680.00 81404 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

Currently, pathogenic variants in TWNK are the only identified cause of IOSCA, and all individuals diagnosed with IOSCA harbored two pathogenic variants in TWNK (Nikali et al. 2005). As a consequence, clinical sensitivity is expected to be high when detecting TWNK defects in patients with this disease. A TWNK defect is also likely in adPEO patients (Fratter et al. 2010). Out of 32 adPEO families, Fratter et al. identified 26 families with pathogenic variants in TWNK (~81%), while the remaining 6 families had defects in either POLG or SLC25A4TWNK-associated mtDNA depletion syndrome has been reported in only five individuals to date, and is likely a rare cause of this disease (Sarzi et al. 2007; Hakonen et al. 2007). Additionally, TWNK defects are an infrequent cause of Perrault syndrome, as only four affected individuals have been described in the literature (Morino et al. 2004).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 TWNK$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Features

Autosomal dominant progressive external ophthalmoplegia (adPEO) is one of several possible clinical manifestations of the mitochondrial DNA (mtDNA) deletion disorders. In TWNK/C10orf2-related adPEO, affected individuals display cytochrome c oxidase (COX)-deficient muscle fibers and multiple mtDNA deletions in skeletal muscle. The primary features of this disease are progressive external ophthalmoplegia (PEO) and ptosis, while other symptoms may include proximal muscle weakness, exercise intolerance, peripheral neuropathy, ataxia, cataracts, cardiomyopathy, and depression (Spelbrink et al. 2001). The sensory ataxic neuropathy, dysarthria, and ophthalmoparesis (SANDO) phenotype has also been reported (Hudson et al. 2005). In a group of adPEO patients from the United Kingdom and Germany, the mean age at onset was 42 years (range: 8-65 years) (Fratter et al. 2010). 

Pathogenic variants in TWNK may also cause recessive, early-onset diseases of mtDNA maintenance, which include infantile-onset spinocerebellar ataxia (IOSCA) and the hepatocerebral form of mtDNA depletion syndrome (MDS) (Fratter et al. 2010).

IOSCA is a severe neurodegenerative disorder. Children with IOSCA typically develop progressive atrophy of the cerebellum, brain stem and spinal cord, in addition to sensory axonal neuropathy (Nikali et al. 2005). After normal development in the first year, children with IOSCA start to develop the following clinical features in successive order: spinocerebellar ataxia, muscle hypotonia, athetoid movements, loss of deep-tendon reflexes, hearing deficiency, ophthalmoplegia, optic atrophy, epileptic encephalopathy, and female primary hypergonadotropic hypogonadism (Koskinen et al. 1994; Koskinen et al. 1994; Nikali et al. 2010).

MDS is a group of clinically and genetically heterogeneous diseases characterized by a quantitative abnormality of the mitochondrial genome (Suomalainen and Isohanni, 2010; El-Hattab and Scaglia, 2013). The hepatocerebral form of MDS commonly presents with severe hepatopathy, hypotonia, and psychomotor delay. Clinical features may also include lactic acidosis, peripheral neuropathy, epilepsy, ophthalmoplegia, nystagmus, athetosis, ataxia, sensorineural hearing impairment, and cerebellar cortical atrophy. The TWNK-related hepatocerebral form of MDS has an early disease onset that presents during the neonatal or infantile periods. 

Finally, pathogenic variants in TWNK have been reported as a rare cause of autosomal recessive Perrault syndrome (Morino et al. 2014). Perrault syndrome is a neurological disorder primarily characterized by gonadal dysgenesis in females and sensorineural hearing loss in both males and females. Additionally, affected individuals may present with ataxia, muscle weakness, ophthalmoplegia, nystagmus, and intellectual disability. To date, only four affected females from two unrelated families have been identified with TWNK-related Perrault syndrome (Morino et al. 2014). Sensorineural hearing loss was diagnosed during childhood in each case. At puberty, affected individuals presented with primary amenorrhea, a failure to develop secondary sexual characteristics, and gonadal dysfunction.

Genetics

The TWNK gene is commonly known as TWINKLE, PEO or PEO1 in the literature. Pathogenic variants in the TWNK gene are the primary known cause of autosomal dominant progressive external ophthalmoplegia (adPEO) (Fratter et al. 2010). TWNK has 5 exons and encodes for a hexameric DNA helicase that assists with mtDNA replication. The majority of TWNK pathogenic variants are missense changes, although at least one small deletion and one large duplication have been reported to date. Most causative TWNK variants are clustered within exon 1 and 2 of the gene, and several de novo pathogenic variants have been reported (Fratter et al. 2010). Pathogenic variants in POLG, SLC25A4, POLG2, RRM2B, and DNA2 can also cause adPEO (Fratter et al. 2010; Ronchi et al. 2013).

Infantile-onset spinocerebellar ataxia (IOSCA) is an autosomal recessive disorder, and pathogenic variants in TWNK are the only identified cause of IOSCA (Nikali et al. 2010). For this disorder, only missense changes and one splicing variant have been reported to date. A major cause of IOSCA is the Finnish founder variant c.1523A>G (p.Tyr508Cys) in exon 3 (Nikali et al. 2005).

The hepatocerebral form of mtDNA depletion syndrome (MDS) is another TWNK-related autosomal recessive disorder. Pathogenic TWNK missense changes have been reported in several unrelated families with the hepatocerebral form of MDS (Sarzi et al. 2007; Hakonen et al. 2007). The POLG, DGUOK, and MPV17 genes are also associated with the hepatocerebral form of this disease (Suomalainen and Isohanni 2010; El-Hattab and Scaglia 2013).

Only two families have been described with TWNK-related autosomal recessive Perrault syndrome to date; in both families, missense changes were identified as causative for disease in affected individuals (Morino et al. 2014). Pathogenic variants in HSD17B4, HARS2, LARS2, and CLPP may also result in Perrault syndrome.

Testing Strategy

Full gene sequencing of TWNK is performed, with bidirectional sequencing of exons 1-5. The full coding region of each exon plus ~20 bp of flanking non-coding DNA on either side are sequenced. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with a known pathogenic variant or to confirm research results.

Indications for Test

Sequencing of TWNK is recommended in all adPEO patients regardless of the results of either muscle biopsy or long-range PCR screen for mtDNA rearrangements (Fratter et al. 2010). Candidates for this test can also be patients with clinical symptoms consistent with IOSCA, the hepatocerebral form of MDS, or Perrault syndrome. Additionally, testing is indicated for family members of patients who have known TWNK pathogenic variants.

Gene

Official Gene Symbol OMIM ID
TWNK 606075
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
Mitochondrial Genome Maintenance/Integrity Nuclear Genes Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • El-Hattab A. and Scaglia F. 2013. Neurotherapeutics. 10:186-98.  PubMed ID: 23385875
  • Fratter C. et al. 2010. Neurology. 74:1619-26. PubMed ID: 20479361
  • Hakonen A.H. et al. 2007. Brain. 130:3032-40. PubMed ID: 17921179
  • Hudson G. et al. 2005.  Neurology. 64:371–3. PubMed ID: 15668446
  • Koskinen T. et al. 1994. Journal of the Neurological Sciences. 121:50-6. PubMed ID: 8133312
  • Koskinen T. et al. 1994. Muscle & Nerve. 17:509–15. PubMed ID: 8159181
  • Morino H. et al. 2014. Neurology. 83: 2054-61. PubMed ID: 25355836
  • Nikali K. and Lönnqvist T. 2010. Infantile-Onset Spinocerebellar Ataxia. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301746
  • Nikali K. et al. 2005. Human Molecular Genetics. 14:2981-90. PubMed ID: 16135556
  • Ronchi D. et al. 2013. American Journal of Human Genetics. 92: 293-300. PubMed ID: 23352259
  • Sarzi E. et al. 2007. Annals of Neurology. 62:579-87. PubMed ID: 17722119
  • Spelbrink JN. et al. 2001. Nature Genetics28:223–31. PubMed ID: 11431692
  • Suomalainen A. and Isohanni P. 2010. Neuromuscular Disorders. 20:429-37. PubMed ID: 20444604
Order Kits
TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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