Genetic Testing for EpilepsyA Guide for Clinicians

KNOWING WHAT TO LOOK FOR KNOWING WHERE TO LOOK AND KNOWING WHAT IT MEANS

Epilepsy

GENE T IC TEST ING FOR EPILEPS IES : A GU IDE FOR CL IN IC IANS 1

Introduction

Epilepsy is a common neurological disorder that affects at least 0.8% of the population. It is defined by the occurrence of at least two unprovoked seizures occurring more than 24 hours apart. Seizures are the manifestation of abnormal hypersynchronous discharges of cortical neurons lasting for several seconds, minutes, or longer. The clinical presentation of seizures depends upon both the location of the epileptic discharges in the cortex and the extent and pattern of propagation of the electrical discharges in the brain.

In many cases, seizures result in convulsions and loss of consciousness. Seizures may also manifest in other ways that affect personality, mood, memory, sensation, and/or movement. Blank stares, lip smacking, intermittent eye movements, and jerking movements of the extremities are all examples of possible manifestations of seizures. In some cases these may not be recognized as a seizure by patients, their family members, or even health care professionals. Seizures can be classified into various categories (Figure 1).

Reference: Cowan, LD. The epidemiology of the epilepsies in children. Ment Retard Develop Disab (2002) 8:171-181.

Etiology

Epilepsy may be an isolated neurological symptom, or it may occur as part of a more complex syndrome. There are many different causes of epilepsy, including genetic disorders, metabolic diseases, and structural brain abnormalities. However, in some cases, the cause of epilepsy is not known. The International League against Epilepsy (ILAE) has described the underlying causes of epilepsy as the following.3

Genetic: “The concept of genetic epilepsy is that the epilepsy is, as best as understood, the direct result of a known or presumed genetic defect(s) in which seizures are the core symptom

Figure 1.

PLEASE REDRAW to make it look similarly to the one in the guide.

Infantile Spasms 1-9%

Absence 5-22%

Generalized Tonic-Clonic 12-24%

Myoclonic 1-11%

Other Generalized <1-3%

Unclassified / Mixed 4-43%

Complex Partial 8-31%

Simple Partial 2-12%

Other Partial 7-29%

FIGURE 1: Types of seizures.

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of the disorder.”3 The genetic contribution must be evident by extensive and replicable molecular studies or familial studies, e.g., SCN1A gene has been demonstrated to be associated with GEFS+.9

Structural/metabolic: If there is a specific structural or metabolic disorder that has been proven in various studies to be associated with increased risk of epilepsy, the cause of epilepsy can be defined as structural or metabolic. The cause for such a disorder can be acquired (e.g., trauma, stroke, infection), genetic (e.g., malformations of cortical development) or both (e.g., West syndrome).

Unknown cause: This means that the underlying cause is yet unknown. Epilepsy might be presenting because of either some genetic defect or as a result of disorder that is not yet recognized.

Diagnosis of Epilepsy

Clinical and family history

The detailed clinical history may help confirm that the seizure events are in fact epileptic seizures, rather than non-epileptic events such as fainting, breath-holding, transient ischemic attacks, strokes, arrhythmias, or hypoglycemia, all of which can manifest similarly to epileptic seizures. A detailed clinical history also may help clarify potential triggers and diurnal patterns related to seizure events. The medical history will help to determine if the seizures are isolated or part of a larger syndrome. In addition to clinical history for the affected individual, a family medical history should be obtained, including any history of seizures and other neurodevelopmental disorders in any relatives. This information may help clarify the type of epilepsy in a family, including the mode of inheritance and the prognosis.

Electroencephalogram (EEG)

Children with a known or suspected diagnosis of epilepsy based on clinical and family history should undergo an EEG to help confirm the seizure type, and to evaluate recurrence risk for future seizures. An EEG may also provide important information for making treatment decisions (Figure 2).

Physical examination

In some cases, an individual with epilepsy may have other related neurological abnormalities, medical problems, or dysmorphic features that can be identified by physical examination. For example, many genetic syndromes involving epilepsy also cause developmental delay, hypotonia, birth defects, ataxia, dystonia, microcephaly or macrocephaly, dysmorphic facial features, or other features that can be noted in a physical examination.

Genetic testing

The information obtained from clinical and family histories, physical examination, and EEG can help a clinician determine whether genetic testing should be offered to a patient with epilepsy and which specific genetic test(s) may be appropriate.2

GENE T IC TEST ING FOR EPILEPS IES : A GU IDE FOR CL IN IC IANS 3

Genetics of Epilepsy

The last decade has witnessed the discovery of many genes involved in epilepsy. Most of these genes are expressed in the brain and encode subunits of ion channels that play vital roles in stabilizing or propagating neuronal activity. Disruption of these genes in general induces neuronal hyperexcitability, thus causing seizures. As described above, there are many forms of epilepsies. A single gene may be associated with different forms of epilepsy, but one type of epilepsy may also result from defects in any one of a variety of genes.5 Inherited channels caused by mutations in ion channel or neuroreceptor genes (e.g., SCN1A-related disorders and KCNQ2, KCNQ3 mutations in benign familial neonatal seizures) can present with seizures.9 Rarely epilepsy syndromes can be the result of severe mutations in single genes whereas more commonly epilepsy is likely to be caused by the combined effect of variants in a number of genes that cannot be currently defined. Examples of monogenic causes of epilepsy are pyridoxine-dependent epilepsy and neuronal ceroid lipofuscinoses (NCL). In some cases, copy number variations associated with neuropsychiatric disorders can be involved in epilepsy too. It is well known that the 1p36 microdeletion, Wolf- Hirshhorn, Miller-Dieker, Pallister-Killian, and Angelman syndromes include epilepsy as a major feature, but these disorders also involve various other clinical features as well.2 Table 1 shows the common genetic disorders that have been associated with epilepsy. Some rare mitochondrial disorders, such as MERRF and MELAS can also present with epilepsy as one of the symptoms.1

Normal EEG (9yr-old child)

Modified hypsarrhythmia during sleep in patient with infantile spasms (8mo-old infant)

Generalized spike wave in patient with absence epilepsy (3yr-old child)

FIGURE 2: Typical EEG abnormalities for different types of seizures.

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Syndrome Clinical Presentation Inheritance Genes

Adenylosuccinate lyase deficiency

Psychomotor delay, intellectual disability, intractable seizures ± autism

AR ADSLI,C,A

Angelman/Angelman-like syndromes

Developmental delay, onset at >6 months of age, ataxia, tremulousness, ‘‘happy’’ appear-ance, microcephaly, seizures

AD CNTNAP2I,C,A SLC9A6I,C,A NRXN1I,C,A TCF4I,C,A UBE3AI,C,A

Autosomal dominant nocturnal frontal lobe epilepsy

Seizures arising from sleep, prominent motor manifestations

AD CHRNA2C,A CHRNA4C,A CHRNB2C,A

Autosomal dominant partial epilepsy with auditory features

Ictal auditory symptoms and receptive aphasia, ± secondary generalization, benign course

AD LGI1C,A

Baltic myoclonus (Unverricht-Lundbord disease)

Individuals in late childhood or adolescence with photosensitive myoclonus, seizures, ataxia

AR CSTBC,A,P

Benign familial neonatal-infantile seizures (BFNIS)

Seizures from 2 days of age to 6 months, normal development

AD SCN2A,I,C

Benign familial neonatal seizures (BFNS)

Neonatal seizures at approximately 3 days of age, resolution at <1 month of age, generalized or focal tonic-clonic seizures, normal development

AD KCNQ2I, KCNQ3I

Creatine deficiency syndromes

Developmental delay, seizures, positive magnetic resonance spectroscopy,± autism

Various GAMTI,C, GATMC SLC6A8C

Early-onset epileptic encephalopathy and/or infantile spasms

Early onset, multiform and intractable seizures, cognitive, behavioral, and neurological

Various ALDH7A1I, ARXI ATP6AP2I CDKL5I,C PCDH19I,C POLGI,C,A PNPOI, SCN1AI,C SLC2A1I,C,A SLC25A22I SPTAN1I STXBP1I

Epilepsy with variable learning and behavioral disorders

Variable clinical presentations with com-binations of epilepsy, learning difficulties, macrocephaly, and aggressive behavior

XL SYN1C,A

Generalized epilepsy with febrile seizures plus (GEFS+)

Onset of febrile seizures at <1 year of age, persistence beyond age 6 years, evolution to mixed seizure types

AD GABRG2I,C SCN1AI,C SCN1BI,C SCN2AI,C

Superscript indicates the panels on which the genes are present. I = infantile epilepsy panel; C = Childhood-onset epilepsy panel; A= Adolescent onset epilepsy panel; P = Progressive myolconic epilepsy panel

Table 1: Genetic disorders associated with Epilepsy

GENE T IC TEST ING FOR EPILEPS IES : A GU IDE FOR CL IN IC IANS 5

Syndrome Clinical Presentation Inheritance Genes

Glucose transporter Type I deficiency syndrome

Early-onset refractory seizures, movement disorders, ataxia, pro-gressive encephalopathy, acquired microcephaly, and spasticity

AD SLC2A1I,C,A

Juvenile Myoclonic Epilepsy (JME)

Typically seizures begin between late childhood and early adulthood, characterized by quick jerks of the arms, shoulder, or occasionally the legs

AD CACNB4C,A EFHC1C,A GABRA1C,A

Lafora disease Progressive myoclonus, myoclonic epilepsy, absences, and dementia

AR EPM2AC,A,P EPM2BC,A,P

Microcephaly with early-onset intractable seizures and develop-mental delay (MCSZ)

Infantile-onset seizures accompanied by microcephaly developmental delay and various behavioral problems (typically hyperactivity)

AR PNKPI

Mowat-Wilson syndrome

Distinctive facial features, Hirschsprung Disease, intellectual disabilities, genital abnormalities, congenital heart disease, agenesis of the corpus callosum, seizures, eye defects and severe speech impairment.

Various ZEB2I,C

Neuronal Ceroid Lipofuscinoses (NCL)

Intellectual and motor deterioration, seizures, visual loss, and early mortality

AR CLN3I,C,A,P CLN5I,C,A,P CLN6I,C,A,P CLN8I,C,A,P CTSDI,C,A,P MFSD8I,C,A,P PPT1I,C,A,P TPPI,C,A,P

Ohtahara syndrome Suppression burst on electroen-cephalogram, tonic seizures

Various STXBP1I, ARXI

Progressive Myoclonic Epilepsy (PME)

Myoclonic seizures, cognitive

impairment, ataxia, and dementia

AR PRICKLE1C,A,P

Pyridoxine depen-dent seizures

Vitamin B6-responsive seizures AR ALDH7A1I

Rett/Atypical Rett syndrome

Rett Syndrome: Regression then stagnation, onset at <18 months of age, loss of purposeful hand move-ments, acquired microcephaly

Atypical Rett Syndrome: Early-onset seizure variant of Rett syndrome, ± Infantile spasms

Various CDKL5I,C FOXG1I,C MECP2I,C

West Syndrome Infantile spasms, hypsar-rhythmia, encephalopathy

Various TSC1I, TSC2I CDKL5I,C, ARXI STXBP1

There are 4 subpanels and a comprehensive panel available to order. ATP1A2 and SRPX2 are not part of any subpanel, but are included in the comprehensive panel along with all the other genes listed in this table.

Superscript indicates the panels on which the genes are present. I = infantile epilepsy panel; C = Childhood-onset epilepsy panel; A= Adolescent onset epilepsy panel; P = Progressive myolconic epilepsy panel

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Clinical Utility of Genetic Testing

Genetic testing for epilepsies is often complex because mutations in so many different genes can cause seizures. Nevertheless, genetic testing can be useful in certain clinical scenarios when it can help in clarifying the prognosis, assist in treatment and management of the patient, and predict the risk of a disease in family members. Genetic testing is termed ‘diagnostic’ if the patient is symptomatic and ‘predictive’ if the patient is asymptomatic, but at risk for having a disorder in the future.1

Utility of genetic testing in treatment:

The treatment of epilepsy depends upon the type of seizure, age of the patient, and other factors. Knowledge of the genetic etiology of epilepsy may guide selection of the most appropriate treatment options in some cases. A number of antiepileptic medications are used in the treatment of epilepsy. The specific type and etiology of seizures may influence the selection of antiepileptic

1. Diagnostic testing in an individual with epilepsy

• Confirm a clinical diagnosis of a specific genetic syndrome or type of epilepsy

• Distinguish between syndromic and non-syndromic forms of epilepsy

• Establish the genetic cause of idiopathic epilepsy

• Provide information about prognosis

2. Assistance with selection of optimal treatment options

3. Predictive testing for asymptomatic family members of a proband with a known disease-causing mutation associated with a genetic form of epilepsy

• Enable clinical monitoring, follow-up, and optimal treatment when symptoms develop in an individual with a positive result

• Reduce anxiety and forego clinical monitoring if result is negative

4. Prenatal diagnosis in at-risk pregnancies for known, pathogenic mutations

5. Genetic counseling, recurrence risk determination, and family planning

TABLE 2: Clinical utility of genetic testing

GENE T IC TEST ING FOR EPILEPS IES : A GU IDE FOR CL IN IC IANS 7

medication for each patient. For example, certain medications may be more effective for infantile spasms and are therefore first choices for patients with spasms. Likewise, certain medications may be contraindicated for patients with a specific electroclinical or genetic diagnosis (Table 3). Dietary modifications including the ketogenic diet are useful in certain conditions1 such as for patients with glucose transporter type 1 deficiency syndrome (SLC2A1 gene).

Disorder Genes Treatment Implications

Alpers-Huttenlocher and other POLG-related disorders

POLG Avoid valproic acid, which can induce or accelerate liver disease

Creatine deficiency syndromes SLC6A8, GAMT, GATM

Oral creatine (GAMT, AGAT)

GEFS+, and other SCN1A-related disorders

SCN1A Valproate, clobazam, stiripentol, leveti-racetam, topiramate. Avoid phenytoin, carbamazepine, and lamotrigine.

Glucose transporter type 1 deficiency syndrome

SLC2A1 Seizures typically respond to a ketogenic diet

Pyridoxal 5’-phosphate-dependent epilepsy

PNPO Seizures respond to treatment with supplemental pyridoxal 5-phosphate (PLP)

Pyridoxine-dependent epilepsy

Folinic-acid responsive seizures

ALDH7A1 Seizures respond to treatment with sup-plemental vitamin B6 and/or folinic acid

Lafora disease EPM2A, EPM2B Avoid phenytoin, lamotrigine, carbamazepine, and oxcarbazepine

Unverricht-Lundborg disease CSTB Avoid sodium channel blockers and GABAergic drugs, which can increase myoclonus, dementia, and ataxia

West syndrome TSC1, TSC2, CDKL5 (STK9), ARX, STXBP1, MEF2C

Vigabatrin for infantile spasms with TSC

TABLE 3: Genetic test results applied to therapeutic decision-making

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Genetic Test Results and What They Mean

There are three possible outcomes of genetic testing: a positive result, a negative result, or a variant of unknown significance (VUS).2

Positive:

A positive result indicates that a disease-causing mutation was identified in the tested individual. This finding confirms the diagnosis of a particular type of epilepsy and provides valuable information to the physician and family members about treatment, prognosis, and recurrence risk. All first-degree relatives (e.g., children, siblings, and parents) of a patient with a positive genetic test result can then be offered predictive genetic testing. If a family member is found to be positive for the familial mutation, this individual is also at risk to develop the epilepsy syndrome and should be referred for further evaluation. It is important to note that there is variability in symptoms, age of onset, severity, and response to therapeutic agents, even among members of the same family who have the same genetic mutation causing epilepsy.

Negative:

A negative result in an individual with epilepsy does not rule out a genetically inherited epilepsy syndrome. Possible reasons for a negative result could be (1) the patient has a mutation in a gene not included in the testing panel, (2) the patient may have a mutation in a part of an epilepsy gene that was not covered by the test, or (3) the patient does not have a heritable form of epilepsy. A negative result obtained in a specific genetic test in an individual with epilepsy indicates that predictive of asymptomatic family members will not be informative for that same test, and is not warranted. However, family members of a clinically affected individual with negative test results may still be at risk for epilepsy syndromes and thus should be evaluated by a neurologist if indicated.

If an asymptomatic individual is negative for a mutation identified in a family member with epilepsy, the result is considered a “true negative.” This indicates that the individual is not at increased genetic risk for the familial epilepsy syndrome and instead has the same risk as a person in the general population to develop seizures. Specific clinical monitoring for the development of seizures is not necessary in individuals with a “true negative” result.

Variant of Unknown Significance:

One of the most difficult results to interpret is the finding of a variant of unknown clinical significance (VUS). This situation indicates that the pathogenic role of the variant cannot be clearly established. In some cases, testing of other family members may help clarify the clinical significance of a VUS. If other relatives with epilepsy are found to have the same variant, it is more likely that the variant is disease-causing. The greater the number of affected family members who carry the VUS, the greater is the likelihood that the VUS is pathogenic. Likewise, if an individual has apparently sporadic epilepsy, the finding that a VUS is de novo (arose new in that individual and was not inherited from a parent) indicates that the variant is likely disease-causing.

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References:

1. Pong, et al. Developments in molecular genetic diagnostics: An update for the pediatric epilepsy specialist, Pediatr Neurol (2011) 44:317-327.

2. Pal, et al. Genetic evaluation and counseling for epilepsy. Nat Rev Neurol (2010) 6:445-453.

3. Berg, et al. Revised terminology and concepts for organization of seizures and epilepsies: Report of the ILAE Commission on Classification and Terminology, 2005-2009. Epilepsia (2010) 51: 676-685.

4. Deprez, et al. Genetics of epilepsy syndromes starting in the first year of life. Neurology (2009) 72:273-281.

5. Baulac, S and Baulac, M. Advances on the genetics of Mendelian idiopathic epilepsies. Neurol Clin (2009) 27:1041-1061.

6. Macdonald, et al. Mutations in GABAA receptor subunits associated with genetic epilepsies. J Physiol (2010) 588:1861-1869.

7. Ottman, et al. Genetic testing in the epilepsies – Report of the ILAE Genetics Commission. Epilepsia (2010) 51:655-670.

8. Ramachandran, et al. The autosomal recessively inherited progressive myoclonus epilepsies and their genes. Epilepsia (2009) 50:29-36.

9. Steinlein, et al. Genetic mechanisms that underlie epilepsy. Nat Rev Neurosci (2004) 5:401-408.

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