Genetic Testing for Epilepsy: Childhood Epilepsy Panel Sequence Analysis and Exon-Level Deletion/Duplication Testing of 58 Genes Panel Gene List: SL, CACNA1A, CDKL5, CHD2, CHRNA2, CHRNA4, CHRNA7*, CHRNB2, CLN3, CLN5, CLN6, CLN8, CNTNAP2, CSTB, CTSD, DYRK1A, EEF1A2, EPM2A, FOLR1, FOXG1**, GABRA1, GABRB2, GABRB3, GABRG2, GAMT, GATM, GOSR2, GRIN1, GRIN2A, IQSEC2, KANSL1, KCNT1, KCTD7, LGI1, MAGI2*, MBD5, MECP2, MEF2C, MFSD8, NHLRC1, NRXN1, PCDH19, PNKP, POLG, PPT1, PRICKLE1, SCN1A, SCN1B, SCN2A, SLC2A1, SLC6A8**, SLC9A6, TBC1D24, TCF4, TPP1, UBE3A, WDR45, ZEB2 *Deletion/duplication testing only (no sequence analysis) for the CHRNA7 and MAGI2 genes *This panel does not include deletion/duplication testing of the FOXG1 or SLC6A8 genes Clinical Features: Epilepsy is defined by the occurrence of at least two unprovoked seizures occurring more than 24 hours apart. It is a common neurological disorder that affects at least 0.8% of the population. The International League against Epilepsy (ILAE) classifies seizures into two main categories. 1 Generalized epileptic seizures originate in and rapidly engage both cerebral hemispheres. Tonic-clonic, absence, myoclonic, clonic, tonic, and atonic seizures are all types of generalized seizures. Focal seizures originate from neuronal networks within a single hemisphere. Traditionally, focal seizures have been classified as simple partial seizures, which do not result in an alteration of consciousness, and complex partial seizures, which cause a change in behavior or consciousness. Some types of seizures, such as infantile spasms, do not fit into either category and remain unclassified. Seizures can be self-limiting or controlled by standard therapeutic treatments in some cases; however, individuals with epileptic encephalopathy have severe seizures that are refractory to treatment, leading to cognitive and behavioral impairment secondary to the epileptic activity. Epilepsy may be an isolated neurological symptom, or it may occur in association with other neurological symptoms or medical problems. 2 Some individuals with epilepsy are diagnosed with an electroclinical syndrome such as febrile seizures plus (FS+) based on the presence of characteristic EEG findings and the clinical and family history. 1 Inheritance Pattern/Genetics: Epilepsy can be caused by genetic disorders, metabolic diseases, trauma, infection, and structural brain abnormalities, although the cause is not known in many cases. A genetic etiology underlies epilepsy in approximately 40% of individuals. 3 Genes have been identified that cause both generalized seizures and focal seizures, as well as unclassified epilepsy types such as infantile spasms. The genetic etiology of idiopathic generalized epilepsy (IGE) is frequently complex because it is due to a combination of multiple genetic factors that each Page 1 of 6, Updated: Dec-16
confer a small risk for epilepsy and may be modified by environmental influences. 3 Currently, approximately 2% of patients with IGE harbor an identifiable pathogenic variant in a single gene associated with Mendelian inheritance of epilepsy. 4 However, the percentage of patients with Mendelian epilepsy is higher for specific epilepsy types such as generalized epilepsy with febrile seizures plus (GEFS+), Lafora disease, and others. 3,5,6,7 The inheritance pattern can be autosomal dominant, autosomal recessive, or X-linked. Pathogenic variants in a single gene may be associated with different types of seizures (clinical heterogeneity), and conversely, pathogenic variants in different genes can cause the same epilepsy phenotype (genetic heterogeneity). The Childhood Epilepsy Panel includes sequencing and deletion/duplication analysis of 58 genes causing Mendelian forms of epilepsy. Many of these genes encode subunits of ion channels involved in stabilizing or propagating neuronal activity, including components of the voltage-gated sodium and calcium channels and the ligand-gated gamma-aminobutyric (GABA) and nicotinic acetylcholine receptor channels. 5,6,7,8 It also includes non-ion channel genes associated with neurotransmitter, storage, and other neurometabolic disorders, as well as genes causing syndromic forms of epilepsy, many of which are involved in transcriptional activation or repression. 5,6,9,10,11 The complete list of genes and associated disorders is included in the table below. Test Methods: Using genomic DNA, coding exons and flanking splice junctions of the genes on this panel are enriched using a proprietary targeted capture method developed by GeneDx. The sequencing component of the test includes all genes in the table above except for CHRNA7 and MAGI2, since only large deletions have been reported in these genes. The products are sequenced on an Illumina instrument using paired end reads. The sequence data is aligned to reference sequences based on human genome build GRCh37/UCSC hg19. Sanger sequencing is used to compensate for low coverage and refractory amplifications. Concurrently, targeted array CGH analysis with exon-level resolution is performed to evaluate for a deletion or duplication of one or more exons for most of the genes included on the panel. If indicated, multiplex ligation-dependent probe amplification (MLPA) of the FOXG1 gene is available as a separate test (test code 904). The presence of any potentially disease-associated sequence variant(s) or copy number alteration(s) is confirmed by dideoxy DNA sequence analysis or quantitative PCR, respectively, or by other appropriate methods. If the Childhood Epilepsy Panel is negative, sequencing and deletion/duplication analysis of the remaining 29 genes on the Comprehensive Epilepsy Panel is available as a separate test. Page 2 of 6, Updated: Dec-16
Test Sensitivity: The clinical sensitivity of sequencing and deletion/duplication analysis of the 75 genes included in the Infantile Epilepsy Panel depends in part on the patient s clinical phenotype. In a prior study, 31% of individuals with infantile spasms who were tested using an epilepsy gene panel were found to harbor definitive pathogenic variant(s) to explain the phenotype (Wirrell et al., 2015). Overall, 17-20% of epileptic encephalopathies have an identifiable genetic etiology (EpiPM Consortium, 2015). Specific information about the diagnostic yield for each gene in selected populations is summarized in the table below. The technical sensitivity of the sequencing test is estimated to be 98%. It will not reliably detect deletions, insertions, or rearrangements greater than or equal to ten base pairs. The deletion/duplication testing can detect deletions or duplications encompassing one or more exons, including variants as small as 150-300 bp. Note that small sections of a few individual genes have inherent sequence properties that yield suboptimal data and variants in those regions may not be identified. Epilepsy Type Gene Protein Inh Diagnostic Yield in Selected Population(s) Familial infantile myoclonic epilepsy (FIME) TBC1D24 TBC1 domain family member 24 AR Unknown 13,14 Early-onset epileptic encephalopathy SCN1A Sodium channel protein type 1 70-80% Dravet syndrome 6 ; 20-24% early-onset cryptic epilepsy 15,16 PCDH19 Protocadherin-19 XL 2-14% females with infantile or childhood epilepsy 17,18,19,20,21 SLC2A1 Solute carrier family 2, facilitated glucose transporter member 1 91% GLUT1 deficiency 3 ; ~10% early-onset absence epilepsy 6 POLG MEF2C DNA polymerase subunit gamma-1 Myocyte-specific enhancer factor 2C AR 63-87% Alpers syndrome 22,23,24 ; 4-5% infantile or childhood epileptic encephalopathy 23 2% epileptic encephalopathy 25 SCN2A Sodium channel protein type 2 1-2% early-onset epileptic encephalopathy 26,27 Page 3 of 6, Updated: Dec-16
KCNT1 Potassium channel, sodium activated subfamily T, member 1 35% MMPSI 68-70 ; Rare in other epileptic encephalopathies 68 CHD2 GABRA1 MAGI2 (dels only) CACNA1A EEF1A2 Chromodomain helicase DNA binding protein 2 receptor subunit -1 Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 Calcium channel, voltagedependent, P/Q type, 1A subunit Eukaryotic translation elongation factor 1 2 1% of epileptic encephalopathy 62 Unknown in Dravet syndrome 67 Unknown 28 Rare 71 Rare 72,73 IQSEC2 IQ motif and sec7 domain 7 XL Rare 71 GRIN1 GABRB2 GABRB3 Glutamate receptor, ionotropic, NMDA 1 (GABA) A receptor, beta 2 (GABA) A receptor, beta 3 Rare 74 Rare 75 Rare 71 Generalized epilepsy with febrile seizures plus (GEFS+) SCN1A Sodium channel protein type 1 SCN1B Sodium channel subunit beta- 1 5-10% GEFS+ 6 <5% GEFS+ 6 GABRG2 receptor subunit gamma-2 <1% GEFS+ 6 SCN2A Sodium channel protein type 2 Rare 5 Autosomal Dominant Focal Epilepsies CHRNA4 Neuronal acetylcholine receptor -4 CHRNB2 Neuronal acetylcholine <5% NFLE 6 ~10% autosomal dominant nocturnal frontal lobe epilepsy (NFLE) 6 Page 4 of 6, Updated: Dec-16
CHRNA2 KCNT1 receptor beta-2 Neuronal acetylcholine receptor -2 Potassium channel, sodium activated subfamily T, member 1 Rare NFLE 6 <5% NFLE 29,30 LGI1 Leucine-rich gliomainactivated protein 1 ~50% autosomal dominant partial epilepsy with auditory features (TLE) 6 Progressive Myoclonic Epilepsy EPM2A Laforin AR 53% Lafora disease 31 NHLRC1 (EPM2B) NHL repeat-containing protein 1 (malin) AR 40% Lafora disease 31 CSTB* Cystatin-B AR >90% Unverricht-Lundborg disease 32 (EPM1) PRICKLE1 Prickle-like protein 1 AR Rare 31 (EPM1B) KCTD7 (EPM3) GOSR2 (EPM6) BTB/POZ domain-containing protein KCTD7 Golgi SNAP receptor complex member 2 AR Rare 33 AR Rare 34,35 FOLR1 Folate receptor AR Rare 36 Idiopathic generalized epilepsy CHRNA7 (dels only) Neuronal acetylcholine receptor subunit -7 ~1% patients with IGE 37 * The dodecamer repeat expansion that accounts for ~90% of all CSTB mutations may not be detectable by this test ** Does not include deletion/duplication testing of FOXG1 and SLC6A8; duplications of GAMT may not be detect References: 1. Berg et al. (2010) Epilepsia 51: 676-685. 2. Pellock, JM (2004) Neurol (2004) 62:S17-S23. 3. Pong et al., (2011) Pediatr Neurol 44:317-327. 4. Weber et al., (2008) Dev Med Child Neurol 50:648-654. 5. Nicita et al., (2011) Seizure: Eur J Epilepsy doi:10.1016/j.seizure.2011.08.007 6. Ottman et al., (2010) Epilepsia 51:655-670. 7. Pal et al., (2010) Nat Rev Neurol 6:445-453. 8. Macdonald et al., (2010) J Physiol 588:1861-1869. 9. Andrade DM (2009) Hum Genet 126:173-193. 10. Ramachandran et al., (2009) Epilepsia 50:29-36. 11. Steinlein et al., (2004) Nat Rev Neurosci 5:401-408. 12. Bennett S. (2004) Pharmacogenomics 5:433-8. 13. Falace et al., (2010) Am J Hum Genet 87:365-370. 14. Corbett et al., (2010) Am J Hum Genet 87:371-375. 15. Zucca et al., (2008) Arch Neurol 65:489-494. 16. Harkin et al., (2007) Brain 130:843-852. 17. Higurashi et al., (2011) Epilepsy Res dio:10.1016/j.eplepsyres.2011.10.014. 18. Depienne et al., (2009) Plos Genet 5(2):e1000381. 19. Marini et Page 5 of 6, Updated: Dec-16
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