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D-2-Hydroxyglutaric Aciduria Type II via the IDH2 Gene - Targeted Variants Analysis

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

Sequencing

Test Code TestIndividual Gene PriceCPT Code Copy CPT Codes
119 IDH2$370.00 81403 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

In a study of 17 unrelated idiopathic D-2-Hydroglutaric Aciduria patients (D2HGA-II) (those with no identified D2HGDH pathogenic variants and normal D-2-HGDH enzyme activity levels), 15 patients were found to be heterozygous for either the p.Arg140Gln (14/15) or p.Arg140Gly (1/15) substitutions, suggesting a clinical sensitivity of ~88% in idiopathic D2HGA-II patients (Kranendijk et al. 2010).

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Clinical Features

D-2-Hydroglutaric Aciduria Type II (D2HGA-II) is a rare inborn error of metabolism caused by a defect in the processing of isocitrate, ultimately resulting in hyperproduction of the metabolite D-2-hydroxyglutaric acid (D2HG). D2HGA-II occurs as a result of specific sequence variants that alter the active site of the mitochondrial isocitrate dehydrogenase-2 (IDH2) enzyme. Affected individuals have presented in infancy or early childhood, usually by 2 years of age, with developmental delay, hypotonia, seizures and dysmorphic features. Approximately half of the reported patients have also presented with cardiomyopathy. Biochemically, D2HGA-II patients are found to have markedly increased levels of D2HG in body fluids (urine, plasma and cerebral spinal fluid), typically higher than the levels observed in D2HGA-I patients (Kranendijk et al. 2010; Nota et al. 2013; Struys et al. 2016). Approximately half of the patients reported with elevated D2HG have been found to have D2HGA-I and the other half have D2HGA-II (Kranendijk et al. 2010).

Pathogenic variants in other genes may also lead to increased levels of D2HG in body fluids. These genes include D2HGDH, IDH1, SLC25A1, and possibly ALDH5A1 and ETFA, ETFB and ETFDH (Struys et al. 2006; Struys et al. 2016). Additional metabolic investigations may be able to distinguish the various causes of elevated D2HG levels.

It should be noted that pathogenic variants in the IDH2 gene have also been reported in patients with a variety of cancers (Kranendijk et al. 2010; Nota et al. 2013; Hamadou et al. 2016). It is not currently clear if D2HGA-II patients are at risk for developing malignancies in the future (Nota et al. 2013).

Genetics

D2HGA-II shows an autosomal dominant mode of inheritance, and is caused by specific pathogenic variants in the IDH2 gene. To date, the only variants that have been shown to be causative for this disorder are p.Arg140Gln (c.419G>A, the most common cause) and p.Arg140Gly (c.418C>G)(Kranendijk et al. 2010; Kranendijk et al. 2011). These pathogenic variants have apparently arisen de novo in the majority of patients, though at least one patient inherited the p.Arg140Gln pathogenic variant from her unaffected mother. Her mother showed somatic mosaicism for the p.Arg140Gln pathogenic variant in her blood, and additional evidence strongly suggested the mother was also germline mosaic for the variant (Kranendijk et al. 2010; Nota et al. 2013).

The IDH2 gene encodes the mitochondrial isocitrate dehydrogenase-2 enzyme, which normally converts the metabolite isocitrate to 2-ketoglutarate (2-KG). The p.Arg140 residue sits within the active site of the IDH2 enzyme. The p.Arg140Gln or p.Arg140Gly missense substitutions alter the function of the enzyme, conferring on it the ability to convert 2-KG to D2HG. This results in hyperproduction of D2HG, which is thought to overwhelm the metabolic capacity of the D-2-hydroxyglutarate dehydrogenase (D2HGDH) enzyme and ultimately result in accumulation of vast amounts of D2HG (Kranendijk et al. 2011; Struys et al. 2016).

Testing Strategy

This test entails bidirectional Sanger sequencing of the IDH2 c.418 and c.419 nucleotides, plus 20 bp of flanking DNA on each side. At this time, sequence IDH2 variants not located at nucleotides c.418 and c.419 will not be reported. We will also sequence this region in family members of patients known or suspected to carry these variants, or to confirm research results that suggest the presence of one of the two targeted variants.

Indications for Test

Patients with clinical and biochemical features consistent with D2HGA-II are good candidates for this test, particularly if they have been shown to have normal D2HGDH enzyme activity and no known pathogenic variants in the D2HGDH gene. Family members of patients who have known IDH2 pathogenic variants may also be good candidates.

This test is specifically designed for the detection of specific heritable germline mutations and is not appropriate for the detection of somatic mutations in tumor tissue.

Gene

Official Gene Symbol OMIM ID
IDH2 147650
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
D-2-Hydroxyglutaric Aciduria 2 AD 613657

Related Tests

Name
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Panel
Organic Aciduria Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Hamadou W.S. et al. 2016. Annals of Hematology. 95: 1943-7. PubMed ID: 27591990
  • Human Gene Mutation Database (Bio-base).
  • Kranendijk M. et al. 2010. Science. 330: 336. PubMed ID: 20847235
  • Kranendijk M. et al. 2011. Biochimica Et Biophysica Acta. 1812: 1380-4. PubMed ID: 21889589
  • Nota B. et al. 2013. Journal of Medical Genetics. 50: 754-9. PubMed ID: 24049096
  • Struys E.A. et al. 2006. Molecular Genetics and Metabolism. 88: 53-7. PubMed ID: 16442322
  • Struys E.A., van der Knapp M.S., Salomons G.S. 2016. 2-Hydroxyglutaric Acidurias. In: Hollak C.E.M. and Lachmann R.H., editors. Inherited Metabolic Disease in Adults: A Clinical Guide. New York: Oxford University Press, p 145-147.
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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.

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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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