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Focal Epilepsy with Speech Disorder with or without Intellectual Disability via the GRIN2A Gene

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

NGS Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
4167 GRIN2A$690.00 81479 Add to Order
Pricing Comment

Our most cost-effective testing approach is NextGen sequencing with Sanger sequencing supplemented as needed to ensure sufficient coverage and to confirm NextGen calls that are pathogenic, likely pathogenic or of uncertain significance. If, however, full gene Sanger sequencing only is desired (for purposes of insurance billing or STAT turnaround time for example), please see link below for Test Code, pricing, and turnaround time information. If you would like to order a subset of these genes contact us to discuss pricing.

For Sanger Sequencing click here.
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 28 days.

Clinical Sensitivity

Three recent studies have identified putative causative mutations in GRIN2A in ~7-12% of patients with FESD (Lesca et al. 2013; Lemke et al. 2013; Carvill et al. 2013). Another study identified pathogenic GRIN2A variants in ~1.5% (2/127) of individuals with a history of idiopathic epilepsy and varying degrees of intellectual disability (Endele et al. 2010).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 GRIN2A$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

Focal epilepsy with speech disorder (FESD) is a neurocognitive disorder characterized by childhood onset of focal seizures, speech disorder and mild to moderate intellectual disability. FESD encompasses a spectrum of epilepsy disorders of varying severities including: Landau-Kleffner syndrome (LKS), Continuous Spike and Waves during Slow-wave Sleep syndrome (CSWSS) and Benign Epilepsy of Childhood with Centrotemporal Spikes (BECTS)/Rolandic Epilepsy. A characteristic feature of FESD-related disorders is centrotemporal spikes or electrical status epilepticus during sleep (ESES) as revealed by EEG recordings (Reutlinger et al. 2010). The presence of ESES during sleep is believed to contribute to cognitive and language impairment, and early treatment with anti-epileptic drugs can lead to improvement of symptoms (Sánchez Fernández et al. 2012). LKS and CSWS are both considered epileptic encephalopathies and have overlapping clinical features including seizures of various types, epileptiform activity during sleep and developmental regression. LKS patients present with seizures at 2-8 years of age and then undergo language regression in the form of aphasia (Caraballo et al. 2013). LKS patients may have delayed speech development and subsequently lose receptive and expressive language. Verbal agnosia, where individuals fail to understand spoken language, is also commonly observed. Seizures and ESES activity remit around the onset of puberty in LKS patients (Sánchez Fernández et al. 2012). CSWS patients present with seizures at 2-4 years of age, and global developmental regression is seen around 5-6 years. Around 10 years of age patients become seizure free and ESES EEG pattern resolves, but neurocognitive impairments persist (Sánchez Fernández et al. 2013). Unlike LKS patients, CSWS patients experience regression in motor skills, language and overall cognitive function. BECTS patients present with seizures during sleep between 7 and 10 years of age. Seizures manifest as a choking sensation, asymmetric clonic spasms of the mouth, drooling and grunting (Sánchez Fernández et al. 2012). Seizures last for 1-2 minutes and 50% of the time consciousness is maintained throughout the episode. Seizures remit during adolescence. BECTS is not associated with developmental regression.

Genetics

FESD is inherited in an autosomal dominant manner and is caused by variations in the GRIN2A gene. Missense, nonsense, splice site and frameshift mutations in GRIN2A have been reported in cases of FESD (Lesca et al. 2013; Lemke et al. 2013; Carvill et al. 2013). The penetrance of GRIN2A variants is incomplete, suggesting that other genetic or environmental factors may act as modifiers of the FESD phenotype. De novo large deletions of 16p13 encompassing GRIN2A have been reported in individuals with intellectual disability, focal seizures and autism spectrum disorders (Reutlinger et al. 2010; Lesca et al. 2012). GRIN2A encodes the alpha-2 subunit (NR2A) of the NMDA receptor and promotes glutamatergic transmission in the central nervous system. NMDA receptors are tetrameric ligand gated ion channels which bind glutamate. The subunit composition of NMDA receptors changes with age, with NR2A present only at later stages of development (Endele et al. 2010). GRIN2A knockout mice exhibit impaired spatial learning and reduced long term potentiation in the hippocampus (Sakimura et al. 1995). It has been proposed that both gain of function and loss of function mutations in GRIN2A result in a similar clinical phenotype (Lemke et al. 2013).

Testing Strategy

For this NextGen test, the full coding regions plus ~20 bp of non-coding DNA flanking each exon are sequenced for the gene listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

Indications for Test

GRIN2A testing should be considered in patients with symptoms of FESD-related disorders such as: idiopathic focal epilepsy, electrical status epilepticus during sleep and acquired aphasia.

Gene

Official Gene Symbol OMIM ID
GRIN2A 138253
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Tests

Name
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Panel
Early Infantile Epileptic Encephalopathy Sequencing Panel
Early Infantile Epileptic Encephalopathy:
Dominant and X-linked Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Caraballo RH, Cejas N, Chamorro N, Kaltenmeier MC, Fortini S, Soprano AM. 2013. Landau–Kleffner syndrome: A study of 29 patients. Seizure. PubMed ID: 24315829
  • Carvill GL, Regan BM, Yendle SC, O’Roak BJ, Lozovaya N, Bruneau N, Burnashev N, Khan A, Cook J, Geraghty E, Sadleir LG, Turner SJ, et al. 2013. GRIN2A mutations cause epilepsy-aphasia spectrum disorders. Nature Genetics 45: 1073–1076. PubMed ID: 23933818
  • Endele S, Rosenberger G, Geider K, Popp B, Tamer C, Stefanova I, Milh M, Kortüm F, Fritsch A, Pientka FK, Hellenbroich Y, Kalscheuer VM, et al. 2010. Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes. Nature Genetics 42: 1021–1026. PubMed ID: 20890276
  • Lemke JR, Lal D, Reinthaler EM, Steiner I, Nothnagel M, Alber M, Geider K, Laube B, Schwake M, Finsterwalder K, Franke A, Schilhabel M, et al. 2013. Mutations in GRIN2A cause idiopathic focal epilepsy with rolandic spikes. Nature Genetics 45: 1067–1072. PubMed ID: 23933819
  • Lesca G, Rudolf G, Bruneau N, Lozovaya N, Labalme A, Boutry-Kryza N, Salmi M, Tsintsadze T, Addis L, Motte J, Wright S, Tsintsadze V, et al. 2013. GRIN2A mutations in acquired epileptic aphasia and related childhood focal epilepsies and encephalopathies with speech and language dysfunction. Nature Genetics 45: 1061–1066. PubMed ID: 23933820
  • Lesca G, Rudolf G, Labalme A, Hirsch E, Arzimanoglou A, Genton P, Motte J, Saint Martin A de, Valenti M-P, Boulay C, Bellescize J De, Kéo-Kosal P, et al. 2012. Epileptic encephalopathies of the Landau-Kleffner and continuous spike and waves during slow-wave sleep types: Genomic dissection makes the link with autism: LKS and CSWSS: Genomic Links with Autism. Epilepsia 53: 1526–1538. PubMed ID: 22738016
  • Reutlinger C, Helbig I, Gawelczyk B, Subero JIM, Tönnies H, Muhle H, Finsterwalder K, Vermeer S, Pfundt R, Sperner J, Stefanova I, Gillessen-Kaesbach G, et al. 2010. Deletions in 16p13 including GRIN2A in patients with intellectual disability, various dysmorphic features, and seizure disorders of the rolandic region: Deletions in 16p13 including GRIN2A. Epilepsia 51: 1870–1873. PubMed ID: 20384727
  • Sakimura K, Kutsuwada T, Ito I, Manabe T, Takayama C, Kushiya E, Yagi T, Aizawa S, Inoue Y, Sugiyama H. 1995. Reduced hippocampal LTP and spatial learning in mice lacking NMDA receptor epsilon 1 subunit. Nature 373: 151–155. PubMed ID: 7816096
  • Sánchez Fernández I, Chapman KE, Peters JM, Harini C, Rotenberg A, Loddenkemper T. 2013. Continuous Spikes and Waves during Sleep: Electroclinical Presentation and Suggestions for Management. Epilepsy Research and Treatment 2013: 1–12. PubMed ID: 23991336
  • Sánchez Fernández I, Loddenkemper T, Peters JM, Kothare SV. 2012. Electrical Status Epilepticus in Sleep: Clinical Presentation and Pathophysiology. Pediatric Neurology 47: 390–410. PubMed ID: 23127259
Order Kits
TEST METHODS

NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most 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 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.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

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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