Forms

Epilepsy: Dravet Syndrome Sequencing Panel

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

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
2659 CHD2 81479 Add to Order
GABRA1 81479
GABRG2 81405
PCDH19 81405
SCN1A 81407
SCN1B 81404
SCN2A 81479
SCN9A 81479
STXBP1 81406
Full Panel Price* $990.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
2659 Genes x (9) $990.00 81404, 81405(x2), 81406, 81407, 81479(x4) Add to Order
Pricing Comment

If you would like to order a subset of these genes contact us to discuss pricing.

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

Extrapolating from previously published studies in large cohorts of patients with Dravet syndrome, we predict that our Dravet syndrome NextGen sequencing panel will identify pathogenic variants in 70-80% of Dravet syndrome patients (Ottman et al 2010; Carvill et al 2014; Gaily et al 2013).

See More

See Less

Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 CHD2$690.00 81479 Add to Order
GABRA1$690.00 81479
GABRG2$690.00 81479
PCDH19$690.00 81479
SCN1A$690.00 81479
SCN1B$690.00 81479
SCN2A$690.00 81479
SCN9A$690.00 81479
STXBP1$690.00 81479
Full Panel Price* $840.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (9) $840.00 81479(x9) 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 Sensitivity

Thus far, no large deletions or duplications have been reported in SCN1B (Human Gene Mutation Database).

See More

See Less

Clinical Features

Dravet syndrome is one of a group of early infantile epileptic encephalopathies (EIEE) which was formerly known as severe myoclonic epilepsy of infancy (SMEI). It is characterized by the onset of seizures within the first year of life in children with previously normal psychomotor development. Early seizures can be clonic or clonic-tonic and are usually brought on by fever. Early EEGs of Dravet syndrome patients reveal no electroclinical abnormalities, but a generalized spike wave pattern is seen as the disease progresses. Dravet syndrome is characterized by the presence of multiple seizure types within patients, including: myoclonic jerks, absence seizures, focal seizures, photosensitive seizures and prolonged seizures resulting in status epilepticus (Akiyama et al. 2012). Seizures observed in Dravet syndrome are resistant to treatment with anti-epileptic drugs. Dravet syndrome patients suffer severe cognitive and motor impairments that persist throughout their lives.

Genetics

This Dravet Syndrome NextGen sequencing panel includes the major-causative gene SCN1A (Ottman et al 2010; Wilmshurst et al 2015), as well as the genes GABRG2, GABRA1, PCDH19, SCN2A, SCN1B, SCN9A, STXBP1 and CHD2. SCN1A encodes an alpha subunit of the voltage-gated sodium channel. Dravet syndrome is mostly caused by loss of function variants in SCN1A in an autosomal dominant manner. The pathogenic variants include missense, nonsense and splice site mutations as well as insertions or deletions that disrupt the reading frame. The majority (94%) of pathogenic variants in SCN1A associated with Dravet syndrome arise de novo (Vadlamudi et al. 2010). Rare cases of inherited Dravet syndrome are seen in situations where the proband's parent was mosaic for the causative SCN1A variant. Causative variants in SCN1A have been reported up to 70 - 80% of patients with Dravet syndrome (Harkin et al. 2007, Ottman et al 2010). Variants in other genes have also been reported to cause Dravet syndrome: GABRA1 encodes a transmembrane subunit of the GABAA receptor. GABAA receptors mediate fast synaptic inhibition in the brain. Dravet syndrome is inherited in an autosomal dominant manner in this gene. De novo pathogenic missense variants were found in Dravet syndrome patients with a rate of 4 out of 67 patients (Carvill et al 2014). GABRG2 encodes a gamma subunit of the GABAA receptor. A heterozygous pathogenic GABRG2 variant was identified in a patient with Dravet syndrome (Huang et al 2012). PCDH19 encodes a protocadherin protein. The disease is inherited in a female-centric X-linked dominant manner. It predominantly affects females due to a process termed 'cellular interference' where populations of cells expressing wild type PCDH19 and cells expressing mutant PCDH19 are required to observe a disease phenotype (Depienne et al. 2009). A pathogenic variant in this gene was detected in 1 case out of 30 Dravet syndrome patients (Gaily et al 2013). SCN2A encodes an alpha subunit of the voltage-gated sodium channel. A heterozygous de novo missense variant was reported to cause Dravet syndrome (Shi et al 2009). SCN1B encodes a beta subunit of the voltage-gated sodium channel. Pathogenic SCN1B variants are rarely identified in patients with Dravet syndrome, but have been reported in a homozygous state (Ogiwara et al 2012). No heterozygous dominant pathogenic variants of SCN1B have been reported in Dravet syndrome (Carvill et al 2014). SCN9A encodes an alpha subunit of the voltage-gated sodium channel. Missense variants in this gene were considered to contribute to complex inheritance of unexplained cases of Dravet syndrome (Mulley et al 2013; Singh et al 2009). STXBP1 encodes syntaxin binding protein 1. Dravet syndrome is inherited in an autosomal dominant manner in this gene. De novo pathogenic missense variants were detected in Dravet syndrome patients with rate of 3 out of 67 patients (Carvill et al 2014). CHD2 encodes a chromodomain helicase DNA-binding protein (CHD). De novo loss of function pathogenic variants were reported in three patients with intellectual disability sharing features with Dravet syndrome (Suls et al. 2013). If you would like to test additional genes, then go to 1) Early Infantile Epileptic Encephalopathy, dominant and X-linked NextGen sequencing panel (24 genes) # 1321 2) Early Infantile Epileptic Encephalopathy NextGen sequencing panel (64 genes) #1961

Testing Strategy

For this NextGen test, the full coding regions plus ~20 bp of non-coding DNA flanking each exon are sequenced for each of the genes 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 and undocumented variants are confirmed by Sanger sequencing.

Indications for Test

Candidates for this panel include patients with symptoms suspicious for Dravet syndrome. This panel is based on recent ILEA recommendation for the management of infantile seizures and also includes additional genes which have been reported to be causative for Dravet syndrome or share phenotypes of Dravet syndrome (Wilmshurst et al 2015).

Genes

Official Gene Symbol OMIM ID
CHD2 602119
GABRA1 137160
GABRG2 137164
PCDH19 300460
SCN1A 182389
SCN1B 600235
SCN2A 182390
SCN9A 603415
STXBP1 602926
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Severe Myoclonic Epilepsy In Infancy 607208

Related Tests

Name
Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Sequencing Panel with CNV Detection
Brugada Syndrome Sequencing Panel
Brugada Syndrome via the SCN1B Gene
Comprehensive Cardiac Arrhythmia Sequencing Panel
Comprehensive Cardiology Sequencing Panel with CNV Detection
Comprehensive Neuropathy Sequencing Panel
Dravet Syndrome and Generalized Epilepsy with Febrile Seizures Plus via the SCN1A Gene
Early Infantile Epilepsies and Autism via the SCN2A Gene
Early Infantile Epileptic Encephalopathy Sequencing Panel
Early Infantile Epileptic encephalopathy-4/Ohtahara syndrome via the STXBP1 Gene
Early Infantile Epileptic Encephalopathy:
Dominant and X-linked Sequencing Panel
Epilepsy and Intellectual Disability in Females via the PCDH19 Gene
Epilepsy: Generalized Epilepsy with Febrile Seizures Plus (GEFS+) Sequencing Panel
Epilepsy: Ohtahara Syndrome Sequencing Panel
Epileptic Encephalopathy and Intellectual Disability via the CHD2 Gene
Episodic Pain Syndrome Sequencing Panel
Familial Atrial Fibrillation Syndrome Sequencing Panel
Familial Hemiplegic Migraine Sequencing Panel
Generalized Epilepsy with Febrile Seizures Plus and Dravet syndrome via the SCN1B Gene
Generalized Epilepsy With Febrile Seizures Plus via the GABRG2 Gene
Juvenile Myoclonic Epilepsy via the GABRA1 Gene
Sodium Channel, Voltage-Gated, Type IX, Alpha Subunit Disorders via the SCN9A Gene
X-Linked Intellectual Disability Sequencing Panel with CNV Detection

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Akiyama M. et al. 2012. Acta Medica Okayama. 66: 369-76. PubMed ID: 23093055
  • Carvill G.L. et al. 2014. Neurology. 82: 1245-53. PubMed ID: 24623842
  • Depienne C. et al. 2009. Plos Genetics. 5: e1000381. PubMed ID: 19214208
  • Gaily E. et al. 2013. Epilepsia. 54: 1577-85. PubMed ID: 23808377
  • Harkin LA. et al. 2007. Brain : a Journal of Neurology. 130: 843-52. PubMed ID: 17347258
  • Huang X. et al. 2012. Neurobiology of Disease. 48: 115-23. PubMed ID: 22750526
  • Human Gene Mutation Database (Bio-base).
  • Mulley J.C. et al. 2013. Epilepsia. 54: e122-6. PubMed ID: 23895530
  • Ogiwara I. et al. 2012. Epilepsia 53: e200–e203. PubMed ID: 23148524
  • Ottman R. et al. 2010. Epilepsia 51:655-70. PubMed ID: 20100225
  • Shi X. et al. 2009. Brain & Development. 31: 758-62. PubMed ID: 19783390
  • Singh N.A. et al. 2009. Plos Genetics. 5: e1000649. PubMed ID: 19763161
  • Suls Arvid et al. 2013. The American Journal of Human Genetics. 93: 967-975. PubMed ID: 24207121
  • Vadlamudi L. et al. 2010. The New England Journal of Medicine. 363: 1335-40. PubMed ID: 20879882
  • Wilmshurst J.M. et al. 2015. Epilepsia. 56: 1185-97. PubMed ID: 26122601
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.
loading Loading... ×