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Autosomal Dominant Nocturnal Frontal Lobe Epilepsy via the CHRNB2 Gene

  • 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
1180 CHRNB2$650.00 81405 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
Mutations in CHRNB2 account for ~5% of familial ADNFLE cases (Ottman et al. Epilepsia 51(4):655-670, 2010).

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Clinical Features
Autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE, OMIM:600513) is a partial seizure disorder characterized by seizures that occur during non-REM sleep. Seizures in ADNFLE patients can present as repetitive limb movements, dystonic posturing, sleep walking, or sudden elevation of the body or head (Kurahashi and Hirose, GeneReviews, 2012). Seizures are brief, lasting from 5 seconds to 5 minutes, and often patients maintain consciousness throughout the attack. Frontal origin of ADNFLE seizures is revealed by ictal EEG recordings; interictal EEGs are normal. ADNFLE associated seizures are often managed with low doses of antieplieptic drugs (AEDs). ADNFLE is not generally associated with cognitive deficits or psychiatric problems, however, recent evidence suggests that a subset of ADNFLE-causing mutations may have wider neurological phenotypes (Steinlein et al. Seizure 21(2):118-123, 2012). ADNFLE can be difficult to clinically distinguish  from other non-epileptic paroxysmal sleep disorders, therefore a video-polysomnography recording brain/eye/muscle activity during sleep is considered essential for diagnosis.
Genetics
ADNFLE is inherited in an autosomal dominant manner. ADNFLE is a genetically heterogeneous disorder.  Mutations in the CHRNB2 gene have been reported in ~5% of individuals with a family history of ADNFLE (Ottman et al. Epilepsia 51(4):655-670, 2010). The penetrance of CHRNB2 mutations is incomplete (~70%), thus ADNFLE presentation can be variable in families (Kurahashi and Hirose, 2012).

CHRNB2 encodes a neuronally expressed beta-subunit of the nicotinic acetylcholine receptor (nAChR). The nAChRs belong to a super-family of ligand-gated ion channels. All of the reported ADNFLE-associated CHRNB2 variants are missense mutations and most are located within the transmembrane domain of the receptor. Highly conserved residues within the transmembrane domain dictate the ligand-specificity and activity of the receptor. Reported mutations in CHRNB2 are gain of function mutations, resulting in an increased sensitivity of neuronal nAChRs to the agonist acetylcholine (Phillips et al. Am J Hum Genet. 68(1):225-231, 2001). It is hypothesized that increased nAchR activity underlies the epilepsy phenotype associated with CHRNB2 mutations.
Testing Strategy
Testing involves PCR amplification from genomic DNA and bidirectional Sanger sequencing of the coding exons and ~20bp of adjacent noncoding sequences. This testing strategy will reveal coding sequence changes, splice site mutations and small insertions or deletions in the CHRNB2 gene, but will not detect large deletions, insertions or rearrangements in the CHRNB2 locus. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.
Indications for Test
Candidates for CHRNB2 sequencing include patients who display symptoms of ADNFLE and who have a family history of nocturnal seizures consistent with an autosomal dominant form of inheritance.

Gene

Official Gene Symbol OMIM ID
CHRNB2 118507
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Epilepsy, Nocturnal Frontal Lobe, Type 3 605375

Related Tests

Name
Autosomal Dominant Nocturnal Frontal Lobe Epilepsy via the CHRNA4 Gene
Familial Focal Epilepsy with Variable Foci via the DEPDC5 Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Kurahashi H, Hirose S. 2012. Autosomal Dominant Nocturnal Frontal Lobe Epilepsy. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301348
  • Ottman R. et al. 2010. Epilepsia 51:655-70. PubMed ID: 20100225
  • Phillips HA, Favre I, Kirkpatrick M, Zuberi SM, Goudie D, Heron SE, Scheffer IE, Sutherland GR, Berkovic SF, Bertrand D. 2001. CHRNB2 Is the Second Acetylcholine Receptor Subunit Associated with Autosomal Dominant Nocturnal Frontal Lobe Epilepsy. The American Journal of Human Genetics 68: 225–231. PubMed ID: 11104662
  • Steinlein, O.K. et al. (2012). "Mutations in familial nocturnal frontal lobe epilepsy might be associated with distinct neurological phenotypes." Seizure 21(2):118:123. PubMed ID: 22036597
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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
  • The first four pages of the requisition form must accompany all specimens.
  • Billing information is on the third and fourth pages.
  • Specimen and shipping instructions are listed on the fifth and sixth pages.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3-5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10-20 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 good for up to 48 hours.
  • If refrigerated, blood specimen is good for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • NextGen Sequencing Tests: Send in screw cap tube at least 10 µg of purified DNA at a concentration of at least 50 µg/ml
  • Sanger Sequencing Tests: Send in a screw cap tube at least 15 µg of purified DNA at a concentration of at least 20 µg/ml. For tests involving the sequencing of more than three genes, send an additional 5 µg DNA per gene. DNA may be shipped at room temperature.
  • Deletion/Duplication via aCGH: Send in screw cap tube at least 1 µg of purified DNA at a concentration of at least 100 µg/ml.
  • Whole-Genome Chromosomal Microarray: Collect at least 5 µg of DNA in TE (10 mM Tris-cl pH 8.0, 1mM EDTA), dissolved in 200 µl at a concentration of at least 100 ng/ul (indicate concentration on tube label). DNA extracted using a column-based method (Qiagen) or bead-based technology is preferred.

CELL CULTURE

(Delivery accepted Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Ship at least two T25 flasks of confluent cells.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We do not culture cells.