Idiopathic Generalized and Focal Epilepsy Panel

Last modified: Jun 12, 2018

Summary

  • Is a 34 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of focal or generalized epilepsy. The genes on this panel are included on the Comprehensive Epilepsy Panel.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

4 weeks

Number of genes

34

Test code

NE1101

Panel size

Large

CPT codes

SEQ 81405
SEQ 81406
SEQ 81407
DEL/DUP 81479

Summary

The Blueprint Genetics Idiopathic Generalized and Focal Epilepsy Panel (test code NE1101):

  • Is a 34 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

ICD codes

Commonly used ICD-10 code(s) when ordering the Idiopathic Generalized and Focal Epilepsy Panel

ICD-10 Disease
G40.00 Focal epilepsy

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

Broadly, epilepsies are divided clinically into generalised and focal forms. The idiopathic/genetic generalized epilepsies, characterized by generalized seizures that involve both sides of the cerebrum, include juvenile myoclonic epilepsy and childhood absence epilepsy among others. These generalized epilepsies tend to start in childhood or adolescence and are usually associated with normal development and intellect. Focal seizures originate in one cerebral hemisphere. Examples of focal epilepsy syndromes are temporal lobe epilepsy, autosomal dominant nocturnal frontal lobe epilepsy, and autosomal dominant epilepsy with auditory features. Genetic factors contribute to both and several monogenic diseases have been detected. Causative mutations in many genes, including some genes coding for ion channel subunits and others involved in synaptic function or brain development, have been identified especially during the past few years. Most of the disease-causing variants are inherited in an autosomal dominant manner, often with incomplete penetrance. The genetic epilepsies are a heterogeneous group. In those patients with known genetic mutations, a significant degree of phenotypic variation and penetrance can be present. Various different epilepsy syndromes may occur within the same family, despite the same genetic mutation. Clinical features and EEG findings, used to define the electroclinical epilepsy syndrome, continues to be a valuable way to classify these disorders in regards to prognosis and treatment. However, genetic diagnosis is needed to fully understand the disease mechanism and it may have an effect to the treatment options.

Genes in the Idiopathic Generalized and Focal Epilepsy Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ALDH7A1 Epilepsy, pyridoxine-dependent AR 50 113
AMACR Alpha-methylacyl-CoA racemase deficiency, Bile acid synthesis defect AR 3 8
CACNA1H Childhood absence epilepsy AD 9 43
CACNB4 Episodic ataxia, Epilepsy, idiopathic generalized, susceptibility to, 9 AD 2 7
CASR Hypocalcemia, Neonatal hyperparathyroidism, Familial Hypocalciuric hypercalcemia with transient Neonatal hyperparathyroidism AD/AR 103 393
CHRNA2 Epilepsy, nocturnal frontal lobe AD 3 6
CHRNA4 Epilepsy, nocturnal frontal lobe AD 7 15
CHRNB2 Epilepsy, nocturnal frontal lobe AD 9 13
CLCN2 Leukoencephalopathy with ataxia, Epilepsy AD/AR 25 23
DEPDC5 Epilepsy, familial focal, with variable foci AD 66 76
EFHC1 Epilepsy, myoclonic juvenile, Epilepsy, severe intractable, Epilepsy, juvenile absence AD/AR 5 34
GABRA1 Epileptic encephalopathy, early infantile, Epilepsy, childhood absence, Epilepsy, juvenile myoclonic AD 23 32
GABRB3 Epilepsy, childhood absence AD 18 41
GABRG2 Generalized epilepsy with febrile seizures plus, Familial febrile seizures, Dravet syndrome, Epilepsy, childhood absence AD 32 32
GRIN2A Epilepsy, focal, with speech disorder AD 52 83
KCNA1 Episodic ataxia/myokymia syndrome AD 24 41
KCNC1 Epilepsy, progressive myoclonic AD 5 2
KCNQ2 Epileptic encephalopathy, early infantile, Benign familial neonatal seizures, Myokymia AD 324 245
KCNQ3 Seizures, benign neonatal AD 18 17
KCNT1 Epilepsy, nocturnal frontal lobe AD 33 37
LGI1 Epilepsy, familial temporal lobe AD 25 49
MTOR Smith-Kingsmore syndrome AD 25 18
POLG POLG-related ataxia neuropathy spectrum disorders, Sensory ataxia, dysarthria, and ophthalmoparesis, Alpers syndrome, Progressive external ophthalmoplegia with mitochondrial DNA deletions, Mitochondrial DNA depletion syndrome AD/AR 90 280
PRRT2 Episodic kinesigenic dyskinesia, Seizures, benign familial infantile, 2, Convulsions, familial infantile, with paroxysmal choreoathetosis AD 40 93
RELN Lissencephaly, Epilepsy, familial temporal lobe AD/AR 23 41
SCN1A Migraine, familial hemiplegic, Epileptic encephalopathy, early infantile, Generalized epilepsy with febrile seizures plus, Early infantile epileptic encephalopathy 6, Generalized epilepsy with febrile seizures plus, type 2 , Febrile seizures, familial 3A AD 654 1489
SCN1B Atrial fibrillation, Brugada syndrome, Generalized epilepsy with febrile seizures plus, Epilepsy, generalized, with febrile seizures plus, type 1, Epileptic encephalopathy, early infantile, 52 AD 15 29
SCN2A Epileptic encephalopathy, early infantile, Seizures, benign familial infantile AD 173 226
SCN8A Cognitive impairment, Epileptic encephalopathy, early infantile AD 92 83
SCN9A Paroxysmal extreme pain disorder, Small fiber neuropathy, Erythermalgia, primary, Geberalized epilepsy with febrile seizures plus, type 7, Insensitivity to pain, congenital, autosomal recessive AD/AR 51 116
SLC2A1 Stomatin-deficient cryohydrocytosis with neurologic defects, Epilepsy, idiopathic generalized, GLUT1 deficiency syndrome AD/AR 98 262
SLC6A1 Myoclonic-astastic epilepsy AD 33 18
STX1B Generalized epilepsy with febrile seizures plus AD 10 9
TBC1D24 Deafness, Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndrome, Deafness, autosomal dominant, 65, Myoclonic epilepsy, infantile, familial, Epileptic encephalopathy, early infantile, 16 AD/AR 41 51

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ALDH7A1 Chr5:125907053 c.696-502G>C NM_001182.4
CASR Chr3:121994640 c.1378-19A>C NM_001178065.1
GABRA1 Chr5:161274418 c.-248+1G>T NM_000806.5
GABRB3 Chr15:27020313 c.-2204G>A NM_000814.5
GABRB3 Chr15:27020399 c.-2290T>C NM_000814.5 rs546389769
SCN1A Chr2:166913031 c.384-21T>A NM_006920.4 rs373168416
SCN1A Chr2:166854699 c.4306-14T>G NM_006920.4
SCN1A Chr2:166848946 c.4820-14T>G NM_006920.4
SCN1A Chr2:166908215 c.964+14T>G NM_006920.4 rs794726837
SLC2A1 Chr1:43395462 c.680-11G>A NM_006516.2

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics idiopathic generalized and focal epilepsy panel covers classical genes associated with generalized epilepsy and focal epilepsy. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.