PGmax^TM - Comprehensive Epilepsy and Seizure Panel

This panel aims to sequences all genes associated with idiopathic and syndromic epilepsy. Included, are those associated with seizures as a major clinical feature or as a minor or variable feature. Importantly, this test only reports variants that fit the mode of inheritance and clinical phenotype of the patient. Patient phenotype information and/or clinical notes are required.

Seizures are caused by abnormal activity in the brain resulting in changes in behavior, motor movements, feelings, or consciousness. Seizures may be triggered by an environmental insult such as head trauma, stroke, or febrile episode or may be the result of a genetic disease. Seizures are classified based on their site of onset: focal, generalized, and unknown (Fisher et al. 2017. PubMed ID: 28276064).

Epilepsy is defined as recurrent unprovoked seizures, and it is divided into subtypes based on the seizures involved: focal, generalized, combined generalized and focal, and unknown (Scheffer et al. 2017. PubMed ID: 28276062). Epilepsy occurs among individuals that are otherwise typically functioning and as a comorbidity in complex neurological diseases. Epilepsy is heterogeneous—there is great variation in the age of onset, type of seizures, developmental outcome, EEG and image findings, response to medication, and associated comorbidities. An epilepsy syndrome refers to a cluster of features incorporating seizure types, together with EEG, and imaging findings (Scheffer et al. 2017. PubMed ID: 28276062).

The etiology of epilepsy is also classified by Scheffer et al. and includes structural, genetic, infectious, metabolic and immune, as well as unknown causes. Importantly, structural and metabolic etiologies may be caused by genetic variants. All etiologies with evidence for genetic causes are included in this panel.

One in 26 people will develop epilepsy in their lifetime (Epilepsy Foundation: epilepsy.com), and the estimated prevalence is 7 per 1,000 (Hirtz et al. 2007 PubMed ID: 17261678). Identifying the molecular basis of a patient’s epilepsy may provide valuable information to inform prognosis, recurrence risk, and treatment. In particular, targeted therapy of genetic epilepsies is an area of rapid change and great promise (see table below). Some patients may benefit from drugs that target a specific pathway, gene product, or functional change to a specific protein (Musto et al. 2020. PubMed ID: 31889633; Reif et al. 2017. PubMed ID: 27781560).

Epilepsy is genetically heterogeneous. Over 350 genes are associated with disorders that include epilepsy as a major feature, and approximately 1,500 genes are associated with disorders that include epilepsy as major, minor, or variable feature.

Genes causative for autosomal dominant, autosomal recessive and X-linked epilepsy and seizures are included in this panel. Mild forms of epilepsy may be inherited as a familial trait; however, many epilepsy cases are sporadic, occurring in families with no prior history of seizure (Allen et al. 2013. PubMed ID: 23934111). Sporadic epilepsy may be inherited by X-linked or autosomal recessive transmission but are more commonly caused by dominant, de novo variants in neuronally-expressed genes. De novo pathogenic missense variants are especially common among genetic epilepsies. For example, missense variants in ion channels (channelopathies) may modify gating kinetics, ion permeability, voltage sensitivity, or ligand-binding imparting both gain- or loss-of-function effects (Kullmann. 2002. PubMed ID: 12023309). In addition, a large number of epilepsy-related genes are sensitive to null mutation, and chain-terminating variants are well-documented to be pathogenic (Human Gene Mutation Database). Finally, rare cases of epilepsy have been attributed to copy number changes involving epilepsy-related genes (i.e., ARHGEF9, ARX, CDKL5, CHD2, DNM1, FOXG1, GABRA1, GABRB3, GABRG2, GRIN2A, MBD5, MECP2, MEF2C, PCDH19, PLCB1, PRRT2, SCN1A, SCN2A, SCN8A, SLC2A1, SLC9A6, SPTAN1, STX1B, STXBP1, TSC1 and TSC2). This test includes CNV analysis. 

This panel contains approximately 1,500 genes associated with syndromic and non-syndromic epilepsy of diverse forms. Examples of well-characterized epilepsy syndromes include developmental epileptic encephalopathies, epilepsy with intellectual disability, metabolic disorders, brain malformation disorders, mitochondrial disorders, brain tumors, etc. (Wilmshurst et al. 2015. PubMed ID: 26122601; Baldassari et al. 2016. PubMed ID: 27208208; Ricos et al. 2016. PubMed ID: 26505888; Møller et al. 2016. PubMed ID: 27781031; de Kovel et al. 2016. PubMed ID: 27652284; Hildebrand et al. 2016. PubMed ID: 27029629; von Spiczak et al. 2017. PubMed ID: 28667181; Hamdan et al. 2017. PubMed ID: 29100083).

Importantly, this panel includes over 26 genes that have been associated with precision therapy in gene-drug studies.

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

Extrapolating from previously published studies of next generation sequencing in large cohorts, a positive test result is expected in the proportions listed: 37% for early infantile epileptic encephalopathy (Della Mina et al. 2015. PubMed ID:24848745; Wang et al. 2014. PubMed ID:24818677; Ream and Mikati. 2014.PubMed ID:25108116), 25-35% for autosomal dominant nocturnal frontal lobe epilepsy, 12-37% for autosomal dominant focal epilepsy (Dibbens et al. 2013. PubMed ID:23542697; Picard et al. 2014. PubMed ID:24814846), 90% for Dravet syndrome (Carvill et al. 2014. PubMed ID:24623842).

The Comprehensive Epilepsy and Seizure Panel offers traditional Patient Only testing as well as options of Family testing (e.g., Duo, Trio, etc) or Patient Plus testing. For Patient Plus, we require specimens from both biological parents along with the patient’s specimen. NGS Panel testing is performed on the patient’s specimen, and targeted Sanger sequencing is performed on parental specimens to determine inheritance, de novo occurrence, and/or phase. For the highest diagnostic rate, Family - Trio testing is recommended.

For the Comprehensive Epilepsy and Seizure Panel we use Next Generation Sequencing (NGS) technologies to cover the coding regions of targeted genes plus ~10 bases of non-coding DNA flanking each exon. As required, genomic DNA is extracted from patient specimens. Patient DNA corresponding to these regions is captured using hybridization probes. Captured DNA is sequenced on the NovaSeq 6000 using 2x150 bp paired-end reads (Illumina, San Diego, CA, USA). The following quality control metrics are generally achieved: 98.2% of target bases are covered at >20x and mean coverage of target bases >100x. Data analysis and interpretation is performed by the internally developed Infinity pipeline. Variant calls are made by the GATK Haplotype caller and annotated using in house software and Jannovar. Common benign, likely benign, and low quality variants are filtered from analysis.

Copy number variants (CNVs) are also detected from NGS data. We utilize a CNV calling algorithm that compares mean read depth and distribution for each target in the test sample against multiple matched controls. Neighboring target read depth and distribution and zygosity of any variants within each target region are used to reinforce CNV calls. All reported CNVs are confirmed using another technology such as aCGH, MLPA, or PCR.

The report will not include all the observed variants in a patient due to the large number of genes included. However, the list of variants is available, along with our interpretations, upon request. 

For tests ordered using the PGnome test method (backbone): individuals will be screened for repeat expansions in FMR1.  Variants in the mitochondrial genome will not be reported at this time.

Of note, Next Generation Sequencing analysis of the SDHA gene is technically challenging due to the presence of segmental duplications and paralogy. Therefore, analysis of CNVs in this region is not included in this test.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).