1. NGS panel - Genetic testing for early infantile epileptic encephalopathy

Early infantile epileptic encephalopathy

July 20, 2017

Clinical features

Epileptic encephalopathies represent a group of severe epileptic diseases with an early onset, characterized by severe electroencephalographic abnormalities and resistance to standard anti-epileptic treatment. According to the International League Against Epilepsy (ILAE) 1, 43 epileptic encephalopathies (EEs) are defined as conditions in which the epileptiform abnormalities are believed to contribute to progressive disturbance in cerebral function, e.g. developmental delay and intellectual disability.

The main clinical features and signs of all epileptic encephalopathies are:

  • Refractory seizures
  • Severe EEG abnormalities
  • Developmental delay/regression or intellectual disability.

Depending on the severity, types of seizures, and prognosis, EEs can be classified into several major subtypes:

Early Infantile EE (EIEE) or Ohtahara Syndrome is one of the most severe forms of EE and is characterized by the following:

  • Presentation within first 3 months of life1, 42 or even earlier, e.g. in utero43
  • Tonic spasms, generalized or lateralized, occurring hundreds times per day and lasting >10s1, 42. About 30% of patients develops other seizure types, such as hemiconvulsions, motor seizures or generalized tonic-clonic seizures42.
  • The EEG is characterized by burst suppression during both wakefulness and sleep
  • Tonic spasms and partial (focal) seizures do not respond to anti-seizure medication
  • Many cases are caused by a brain malformation, metabolic disorder or genetic mutations
  • Ohtahara syndrome is very rare
  • Prognosis of the disease is poor, and patients usually die during infancy.

West syndrome or Infantile spasms (IS) is the most common type of EE and is characterized by a triad of symptoms: spasms, hypsarrhythmia, and developmental delay/regression.

  • IS spasms are brief seizures with flexion or extension of extremities and/or body that occur in clusters upon awakening
  • IS onset is between 3-7 months of age43
  • The estimated incidence is 2-3.5 per 10,000 live births1, 43
  • IS can be associated with malformations of cortical development and hypoxic-ischemic encephalopathy, as well as disorders including tuberous sclerosis and Down syndrome
  • Many patients develop other seizure types
  • The prognosis of the infantile spasms can be improved with early treatment.

Lennox–Gastaut syndrome (LGS) is a childhood onset severe epileptic encephalopathy characterized by multiple seizure types and is characterized by the following:

  • Tonic seizures are always present together with atonic and atypical absence seizures, and focal myoclonic and generalized tonic–clonic seizures
  • The onset of LGS is mostly between 3-5 years of age43
  • The incidence of LGS is estimated to be 1-10% of all childhood-onset epilepsies43
  • EEG shows fast activity paroxysms and generalized slow spike-and-wave discharges
  • Affected LGS patients have different degrees of developmental delay and they often develop autism and intellectual disability43
  • Patients react well to several antiepileptic drugs (clonazepam, felbamate, lamotrigine, topiramate, rufinamide, and clobazam)43.

Severe Myoclonic Epilepsy in Infancy or Dravet Syndrome is a severe form of EE with the following features:

  • Onset is commonly during the first year of life
  • Seizure types include myoclonus, prolonged convulsive seizures, frequent status epilepticus, and febrile seizures
  • The incidence of Dravet syndrome is 0.5–1/40,000 and accounts for up to 8 % of all epilepsies in the first 3 years of life43
  • Most commonly it is caused by mutations of SCN1A gene, encoding the neuronal voltage-gated sodium channel1,3,43.

Early myoclonic encephalopathy is a rare malignant epilepsy syndrome characterized by myoclonus with or without focal motor seizures:

  • Onset occurs very early, just a few hours after birth
  • Seizures are myoclonic, but other types of seizures are also common (partial seizures, massive myoclonia and tonic spasms)
  • The disease is most commonly inherited in an autosomal recessive manner
  • There is no effective treatment for early myoclonic encephalopathy and prognosis is very poor
  • The disease is very rare, with only 30 cases reported so far43
  • A common cause for the disease is mutations in the SLC25A22 gene1,3.

Malignant Migrating Partial Seizures of Infancy (MMPSI) also known as Early Infantile Epileptic Encephalopathy 14 (EIEE14) is a severe form of EE that begins very early in life. MMPSI is clinically characterized by the following:

  • Recurrent seizures in MMPSI commonly start within a few weeks of birth43
  • The seizures in MMPSI are partial or focal
  • Seizure activity can appear in multiple locations in the brain, or migrate from one region to another during an episode
  • Persistent seizures affect brain development and growth, leading to microcephaly43, profound developmental delay, and intellectual disability
  • Seizures are usually refractory to treatment and the majority of affected children do not survive past
  • The disease is very rare, with less than 100 reported cases42,43
  • Mutations in the KCNT1 gene are the most commonly known cause of MMPSI3,26.

Landau-Kleffner syndrome (LKS) is a less severe early epileptic encephalopathy syndrome of mid-childhood and is characterized by the gradual inability to understand and use spoken language43. Major clinical findings of LKS include the following:

  • Language regression
  • EEG abnormalities, including continuous or near-continuous spike-waves during slow wave sleep
  • The age of onset is between 3-7 years of age, boys are affected twice as often as girls43
  • Mutations in the GRIN2A gene have been reported as a major genetic cause of LKS18,19
  • LKS responds to anti-epileptic drugs.

Continuous Spike-Wave during Slow Sleep (CSWS) is an epileptic encephalopathy of childhood characterized by cognitive or behavioral impairment caused by interictal epileptiform discharges during sleep. CSWS seizures commonly present at 2-4 years of age.

  • The seizures are typically unilateral, tonic-clonic or clonic, occurring during the wake phases
  • At the age 5-6 years the seizures become more frequent, severe, and treatment-resistant
  • Developmental regression is common
  • Spontaneous improvement of disease symptoms can occur before adolescence, but most patients remain severely developmentally impaired.

Myoclonic status in nonprogressive encephalopathies (MSNE) is another type of EE and it is characterized by the early onset of continuous diffuse epileptiform abnormalities.

  • The prevalence of MSNE is estimated to be 0.5 %-1 % of all children with severe forms of epilepsy43
  • MSNE is frequently associated with Angelman syndrome, fetal/neonatal brain hypoxia and structural brain malformations
  • Prognosis of MSNE is poor, with progressive neurodegeneration
  • There is no effective treatment except for the benzodiazepines temporary interruptions of the myoclonic status epilepticus.

Development of new technologies in molecular diagnostics, including next generation sequencing (NGS), has resulted in the identification of a number of known monogenic causes underlying the epileptic encephalopathies. Different genetic causes and molecular pathways have been identified so far, including genes encoding the proteins of the ion channels, synaptic proteins, and others, involved in neuronal development, differentiation and other functions. The list of genes included in CENTOGENE´s Early infantile epileptic encephalopathy panel is presented in the table.


Overview of genes included in the Early infantile epileptic encephalopathy panel offered by CENTOGENE

Gene
(OMIM)
chr. locus Mutation frequency Associated/allelic disorders
AARS
(601065)
16q22.1 Rare (2 families)2 EIEE29 (616339); CMT2N (613287)
ALG13
(300776)
Xq23 1/216 for Lennox-Gestaut syndrome3 EIEE36 (300884); Lennox-Gastaut syndrome, West syndrome, CDG1
ARHGEF9
(300429)
Xq11.1 Rare for EIEE3
1/23 boys with MRX4
EIEE8 (300607)
ARV1
(611647)
1q42.2 Rare for EIEE5 EIEE38 (617020)
ARX
(300382)
Xp21.3 1/11 EIEE in China6
1/12 families for West1
Common for MRX, LISX1
EIEE1 (308350); MRX29 (300419); LISX2 (300215); PRTS (309510); Proud syndrome (300004)
CACNA1A
(601011)
19p13.13 >95% for EA7
7% (3/42) for FHM8
99% for SCA69
Common for EIEE3
EIEE42 (617106); SCA6 (183086); EA2 (108500); FHM1 (141500)
CDKL5
(300203)
Xp22.13 4/49 for EIEE1,10
Common in Rett-like syndrome and MR/MRX1,3
EIEE2 (300672); Rett-like syndrome
DNM1
(602377)
9q34.11 5/429 for EE11 EIEE31 (616346)
DOCK7
(615730)
1p31.3 Rare for EIEE (3 patients)12 EIEE23 (615859)
EEF1A2
(602959)
20q13.33 Few families identified13 EIEE33 (616409); MRD (616393)
FGF12
(601513)
3q28-q29 2 families14 EIEE47 (617166)
FRRS1L
(604574)
9q31.3 Few families15 EIEE37 (616981)
GABRA1
(137160)
5q34 2/49 for EIEE3 EIEE19 (615744); EJM5 (611136)
GABRB1
(137190)
4p12 Few families for EIEE16 EIEE45 (617153)
GABRB3
(137192)
15q12 2/49 for EIEE3 EIEE43 (617113); ECA5 (612269)
GNAO1
(139311)
16q13 6 patients with EIEE17 EIEE17 (615473)
GRIN2B
(138252)
12p13.1 Few patients with EIEE18
4/468 for MRD19
4/2446 for ASD19
EIEE27 (616139); MRD6 (613970)
GRIN2D
(602717)
19q13.33 Few patients with EIEE20 EIEE46 (617162)
GUF1
(617064)
4p12 3 patients with EIEE21 EIEE40 (617065)
HCN1
(602780)
5p12 6 patients with EIEE22 EIEE24 (615871)
ITPA
(147520)
20p13 7 patients with EIEE23 EIEE35 (616647); ITP deficiency (613850)
KCNA2
(176262)
1p13.3 1,7% for EIEE24 EIEE32 (616366)
KCNB1
(600397)
20q13.13 3/359 for EIEE13 EIEE26 (616056)
KCNQ2
(602235)
20q13.33 3/49 for EIEE3
60%-80% for BFNS25
20%-40% large del. for BFNS25
EIEE7 (613720); BFNS1 (121200)
KCNT1
(608167)
9q34.3 <5% for ENFL26
3/49 for EIEE3
EIEE14 (614959); ENFL5 (615005)
NECAP1
(611623)
12p13.31 1 family with EIEE27 EIEE21 (615833)
PCDH19
(300460)
Xq22.1 15/150 females with EIEE28 EIEE9 (300460)
PIGA (311770) Xp22.2 Few families for EIEE29
Common for PNH29
EIEE20 (300868); PNH1 (300818)
PLCB1
(607120)
20p12.3 Few patients for EIEE3 EIEE12 (613722)
PNKP
(605610)
19q13.33 Rare for EIEE30
8 families with AOA30
AOA4 (616267); MCSZ (613402)
SCN1A
(182389)
2q24.3 12/49 for EIEE3
Common for GEFSP and FHM1
EIEE6 (607208); GEFSP2 (604403); FHM3 (609634)
SCN2A
(182390)
2q24.3 6/49 for EIEE3 EIEE11 (613721); BFIS3 (607745)
SCN8A
(600702)
12q13.13 Common for EE31
3/49 for EIEE3
EIEE13 (614585); BFIS5 (617080); CIAT (614306)
SCN9A
(603415)
2q24.3 50%-100% for SFN32
2 patients with EIEE1, 3
EIEE6 (607208); SFN (133020); GEFSP7 (613863); CIP (243000); PEPD (167400)
SIK1
(605705)
21q22.3 6 patients with EIEE13,33 EIEE30 (616341)
SLC12A5
(606726)
20q13.12 2 families with EIEE34 EIEE34 (616645); EIG14 (616685)
SLC13A5
(608305)
17p13.1 3 families with EIEE35 EIEE25 (615905)
SLC1A2
(600300)
11p13 2 patients with EIEE36 EIEE41 (617105)
SLC25A12
(603667)
2q31.1 Few patients with EIEE1,3 EIEE39 (612949)
SLC25A22
(609302)
11p15.5 Few patients with EIEE1,3 EIEE3 (609304)
SLC35A2
(314375)
Xp11.23 3 patients with CDG37 EIEE22/CDG2M (300896)
SPTAN1
(182810)
9q34.11 Few patients with EIEE1,3 EIEE5 (613477)
ST3GAL3
(606494)
1p34.1 >5 families qith EIEE38 EIEE15 (615006); MRT12 (611090)
STXBP1
(602926)
9q34.11 Few patients with EIEE1 EIEE4 (612164)
SZT2
(615463)
1p34.2 Few patients with EIEE1,39 EIEE18 (615463)
TBC1D24
(613577)
16p13.3 Few patients with EIEE1
9/18 families with DOORS40
EIEE16 (615338); FIME (605021); DOORS (220500); DFNA65 (616044); DFNB86 (614617)
UBA5
(610552)
3q22.1 5 patients with EE41 EIEE44 (617132); SCA24 (617133)
WWOX
(605131)
16q23.1-q23.2 Few patients with EIEE1 EIEE28 (616211); SCA12 (614322); Esophageal cancer (133239)

Abbreviations for Table 1: EIEE – Early infantile epileptic encephalopathy; Lennox-Gastaut syndrome, West syndrome, CDG – Congenital disorder of glycosylation, MRX – X-linked mental retardation; LISX - Lissencephaly, PRTS – Partington syndrome; Proud syndrome; EA - Episodic ataxia; FHM – Familial hemiplegic migraine; EE – Epileptic encephalopathy; MRD- Mental retardation autosomal dominant; EJM – Juvenile myoclonic epilepsy; ECA – Childhood absence epilepsy; BFNS – Benign familial neonatal seizures; ENFL – Epilepsy nocturnal frontal lobe; PNH - Paroxysmal nocturnal hemoglobinuria; AOA – Ataxia-oculomotor apraxia; MCSZ – Microcephaly seizures and developmental delay; GEFSP – Generalized epilepsy with febrile seizures plus; CIAT – Cognitive impairment with or without cerebellar ataxia; SFN - Small fiber neuropathy; CIP – Congenital insensitivity to pain; PEPD – Paroxysmal extreme pain disorder; EIG – Epilepsy idiopathic generalized; MRT – Mental retardation autosomal recessive; FIME – Familial infantile myoclonic epilepsy; DOORS – DOOR syndrome; DFNA – Deafness autosomal dominant; DFNB – Deafness autosomal recessive.

Even though there are numerous anti-epileptic drugs routinely used for the treatment of epileptic encephalopathies, Ohtahara syndrome seizures are usually difficult to control. Commonly used medications include clobazam, clonazepam, topiramate, phenobarbital, valproate, and others. Some affected children have displayed a good response to steroid therapy with ACTH or prednisone. In addition, epilepsy-related surgery may be helpful in children with localized/focal seizures.

CENTOGENE offers full gene sequencing and deletion/duplication analysis for the Early infantile epileptic encephalopathy panel (genes: AARS, ALG13, ARHGEF9, ARV1, ARX, CACNA1A, CDKL5, DNM1, DOCK7, EEF1A2, FGF12, FRRS1L, GABRA1, GABRB1, GABRB3, GNAO1, GRIN2B, GRIN2D, GUF1, HCN1, ITPA, KCNA2, KCNB1, KCNQ2, KCNT1, NECAP1, PCDH19, PIGA, PLCB1, PNKP, SCN1A, SCN2A, SCN8A, SCN9A, SIK1, SLC12A5, SLC13A5, SLC1A2, SLC25A12, SLC25A22, SLC35A2, SPTAN1, ST3GAL3, STXBP1, SZT2, TBC1D24, UBA5, WWOX).


Differential diagnosis

The differential diagnosis of early infantile epileptic encephalopathy-related disorders – depending on the major symptoms in the initial case – includes the following diseases:

  • Benign childhood epilepsy
  • Complex partial seizures
  • Epilepsia partialis continua
  • Generalized tonic-clonic seizures
  • Autism
  • Acquired epileptic aphasia
  • Absence seizures
  • Temporal lobe epilepsy

Testing strategy

CENTOGENE offers an advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on PCR-free whole genome sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and providing sequencing of the entire gene with more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for early infantile epileptic encephalopathy using NGS Panel Genomic targeted towards this specific phenotype

Step 1: Whole genome sequencing from a single filter card.The sequencing covers the entire gene (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the Early infantile epileptic encephalopathy panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no mutation is identified after analysis of the Early infantile epileptic encephalopathy panel, we further recommend continuing the bioinformatics analysis of the data using whole genome sequencing to cover those genes which are either implicated in an overlapping phenotype or could be involved in a similar pathway but are not strongly clinically implicated based on the current information in literature.


Referral reasons

The following individuals are candidates for early infantile epileptic encephalopathy testing:

  • Individuals with a family history of early infantile epileptic encephalopathy and presentation of the most common symptoms, including early onset seizures
  • Individuals without a positive family history of EIEE, but with symptoms resembling epileptic encephalopathy
  • Individuals with a negative but suspected family history of EIEE, in order to perform proper genetic counseling.

Test utility

Sequencing, deletion/duplication of the panel genes should be performed in all individuals suspected of having early infantile epileptic encephalopathy and suspected phenotypes. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of mutations, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of the early infantile epileptic encephalopathy and related disorders identify at-risk family members, provide disease risks as well as appropriate referral for patient support and/or resources.


More information on CENTOGENE´s Early infantile epileptic encephalopathy panel can be found in our genetic test catalogue.