Epilepsy: A Comprehensive Textbook
2nd Edition
© 2008 Lippincott Williams & Wilkins
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Chapter 15
Genetic Epidemiology
Ruth Ottman
Melodie R. Winawer
Introduction
A genetic contribution to the epilepsies has been suspected for centuries, but until recently, progress in elucidating the specific genetic influences was relatively slow. This slow progress was attributed in part to methodologic problems in research design and analysis, and in part to inherent complexity in the role that genetic factors play in increasing the risk for epilepsy. With the rapid development of research tools in molecular genetics, however, significant advances have been made over the last 10 years, and a number of genes that influence risk for either idiopathic or symptomatic epilepsy syndromes have been identified. Despite these very important advances, most epilepsy is not explained by mutations in these genes, and efforts to identify other genetic influences are continuing.
Identification of genes that influence risk for epilepsy has great implications for public health. It is a first step in investigating the physiologic effects of the susceptibility genes, which can lead to a better understanding of pathogenesis of epilepsy and to new strategies for treatment and prevention. It also facilitates early identification and treatment of susceptible individuals, and perhaps someday, even prevention of epilepsy in some people. See Chapters 17 and 18 for further discussion of these and other related issues.
Gene discoveries also raise important ethical and social issues. For example, when is it appropriate to offer genetic testing, who should offer it, and how should the results be presented to patients (e.g., by the treating physician or a genetic counselor)? These issues have only begun to be considered as the pace of discoveries in genetic research on the epilepsies increases. Some of these issues are discussed in Chapter 19.
Genetic Influences on the Epilepsies: Current Knowledge
So far, almost all of the progress in epilepsy gene identification has come from analysis of rare families with mendelian modes of inheritance (autosomal dominant, autosomal recessive, or X-linked). As of December 2005, 12 genes had been identified in autosomal dominant forms of eight idiopathic epilepsy syndromes (Table 1). All but two of these genes encode voltage-gated or ligand-gated ion channels. In families with benign familial neonatal seizures, mutations have been found in the potassium channel genes KCNQ2 and KCNQ3.18,106 Mutations in the genes encoding three sodium channel subunits, SCN1A, SCN1B, and SCN2A, have been found in different families with generalized epilepsy with febrile seizures plus (GEFS+),30,107,111,112,126 and mutations in SCN2A have also been found in families with a different phenotype, benign familial neonatal-infantile seizures.12,43 Mutations in GABRG2, the gene encoding the γ-2 subunit of the γ-aminobutyric acid subtype A (GABAA) receptor, have been found in families with GEFS+10,38 and in families with childhood absence epilepsy with febrile seizures.50,125 In a large French Canadian family with an autosomal dominant form of juvenile myoclonic epilepsy (JME), a mutation was identified in GABRA1, encoding the α-1 subunit of the GABAA receptor.21 Mutations in EFHC1, encoding a protein with an EF-hand motif that appears to influence calcium currents, were identified in another set of families with JME.114 In three families with an autosomal dominant form of idiopathic generalized epilepsy (IGE) with a range of different syndromes, mutations were identified in the chloride channel gene CLCN2.40 Mutations have been found in the genes encoding two subunits of the neuronal nicotinic acetylcholine receptor (CHRNA4 and CHRNB2) in families with autosomal dominant nocturnal frontal lobe epilepsy.22,108 In families with autosomal dominant partial epilepsy with auditory features (ADPEAF), mutations have been found in the leucine-rich glioma inactivated 1 gene (LGI1), which encodes a leucine-rich repeat protein.49,62,88 The mechanism by which LGI1 influences epilepsy risk is still not well understood, but based on protein homology, it appears likely to be involved in development of the central nervous system.49
Genes have also been identified in a number of mendelian symptomatic epilepsy syndromes. These include progressive myoclonic epilepsies (e.g., Unverricht Lundborg disease, Lafora disease, and the neuronal ceroid lipofuscinoses104), X-linked myoclonic epilepsy with mental retardation,109 and cortical malformation syndromes such as polymicrogyria, pac-hygyria, and periventricular nodular heterotopia.35,61 In addition, mutations in SCN1A have been identified in many patients with severe myoclonic epilepsy of infancy (SMEI).19,69,110,124
Despite the clear importance of these gene discoveries, they apply to only a small proportion of people with epilepsy. Most people with epilepsy have no affected relatives, and only a tiny fraction come from families with mendelian modes of inheritance. In the Epilepsy Family Study of Columbia University (EFSCU),79,83,86,87 we collected family history information on 1,957 people with epilepsy, ascertained from voluntary organizations for epilepsy without regard to their family histories. The proportion of subjects with a positive family history (with one or more first-degree relatives with epilepsy) was 15% in those with IGE and 12% in those with cryptogenic localization-related epilepsy (LRE). Moreover, most of those with a family history had just one affected relative (probands with IGE 77%, cryptogenic LRE 79%), and very few families appeared consistent with a mendelian mode of inheritance.81
Table 1 Mendelian Idiopathic Epilepsy Syndromes with Genes Identified by Positional Cloning (as of December, 2005)
Epilepsy syndrome Gene Chromosomal location References
Benign familial neonatal seizures KCNQ2 20q13 106
  KCNQ3 8q24 18
Generalized epilepsy with febrile seizures plus SCN1B 19q13 126
  SCN1Ab 2q24 30,111
  SCN2Aa 2q24 112
  GABRG2a 5q31 10,38
Benign familial neonatal-infantile seizures SCN2Aa 2q24 12,43
Childhood absence epilepsy with febrile seizures GABRG2a 5q31 50,125
Autosomal dominant juvenile myoclonic epilepsy GABRA1 5q34 21
  EFHC1 6p12 114
Autosomal dominant idiopathic generalized epilepsy CLCN2 3q26 40
Autosomal dominant nocturnal frontal lobe epilepsy CHRNA4 20q13 108
  CHRNB2 1q21 22
Autosomal dominant partial epilepsy with auditory features LGI1 10q24 49,62
a Mutations identified in more than one epilepsy syndrome.
b Mutations (many of which are de novo) also identified in severe myoclonic epilepsy of infancy.
In the large group of people with nonmendelian forms of epilepsy, the genetic influences on risk probably consist mainly of “complex” disease genes—that is, genes with only a small effect, which act additively to raise risk, possibly in combination with environmental factors.70 Research is under way to identify these complex epilepsy genes, but progress has been slow and few findings have been confirmed.116 Given that most of the genes identified in families with mendelian inheritance so far have encoded voltage-gated or ligand-gated ion channels, variants in ion channel genes may well contribute to risk for genetically complex epilepsies also.
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Other types of genetic effects may also play a role in some cases. First, some “sporadic” epilepsies (i.e., those occurring in the absence of a family history) may be caused by de novo mutations. This mechanism is important in SMEI, where many of the mutations identified in SCN1A have been de novo.19,69,110,124 Second, some epilepsies may be caused by somatic mutations occurring in critical brain regions. Third, mitochondrial genetic defects have been demonstrated to underlie disorders in which epilepsy is a significant part of the phenotype (myoclonus epilepsy with ragged red fibers [MERRF] and mitochondrial encephalomyopathy with lactic acidosis and strokelike episodes [MELAS]),24 and could be involved in other forms of epilepsy as well.82 Finally, some of the genetic influences on epilepsy may involve either genomic imprinting, in which expression of a genotype is influenced by the sex of the parent from whom it is inherited,36 or trinucleotide repeat expansion, involving an amplification of the number of tandem repeats in a DNA sequence rather than a change in the nucleic acid sequence per se.115
Complexities in the Genetics of the Epilepsies
The search for genetic contributions to epilepsy is complicated by a number of factors. The relations between genotype (i.e., the genes that influence risk) and phenotype (i.e., the detectable clinical signs and symptoms) in the epilepsies are not at all straightforward. Even in the genes identified in families with mendelian forms of epilepsy, most of the identified mutations have reduced penetrance: Some of those who inherit the mutation are unaffected. This implies that some other factor—an environmental exposure or genotype at a different locus—is required for phenotypic expression of the mutation. Consequently, in families with multiple affected individuals, one cannot assume that unaffected individuals do not carry a susceptibility gene. A special case of this is age-related penetrance: Because risk for epilepsy increases with age, gene carriers may be unaffected if studied at young ages.
Another complication is etiologic and genetic heterogeneity. The epilepsies are extremely clinically heterogeneous, varying by seizure types, ages at onset, brain localization, electrophysiologic and neuroanatomic abnormalities, response to treatment, and many other factors. These differences are so striking that most epileptologists view the epilepsies as a collection of different disorders, or syndromes, with different etiologies. But to what extent do the different clinical entities also differ with respect to their genetic contributions? Which features can best be used to separate the epilepsies into subgroups likely to share susceptibility genes? The answers to these questions are still unknown. Discovery of clinical features that distinguish between epilepsies with larger and smaller genetic contributions and investigation of shared and distinct genetic contributions to different types of epilepsy are important research goals. Such distinctions could aid in the design of studies aimed at gene identification and greatly refine classification of syndromes.
With locus heterogeneity, different genes influence the risk for the same epilepsy syndrome; hence, different families with the same syndrome carry mutations in different susceptibility genes. This phenomenon is well documented in the epilepsies. Multiple autosomal dominant susceptibility genes have been identified in four syndromes: Benign familial neonatal seizures (KCNQ2 and KCNQ3), autosomal dominant nocturnal frontal lobe epilepsy (CHRNA4 and CHRNB2), GEFS+ (SCN1A, SCN1B, SCN2A, and GABRG2), and autosomal dominant JME (GABRA1 and EFHC1). Moreover, different genetic mechanisms—single gene versus complex—can produce the same syndrome in different families, making it impossible to classify syndromes according to genetic mechanisms. For example, the IGEs are genetically complex in most cases, but some families have autosomal dominant inheritance.21,40,114 Although mutations in LGI1 have been found in 50% of families containing two or more subjects with temporal lobe epilepsy with ictal auditory symptoms,88 most patients with these symptoms are sporadic and do not have LGI1 mutations.15,32
Another complication is variable expressivity, in which a mutation in a single gene produces different epilepsy phenotypes in different individuals. For example, in GEFS+, the seizure disorders in family members who have inherited the same SCN1A mutation can vary from simple febrile
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seizures, febrile seizures plus (in which febrile seizures persist beyond age 6 or are accompanied by afebrile generalized tonic–clonic seizures), idiopathic generalized epilepsy, temporal lobe epilepsy, or myoclonic-astatic epilepsy.107 This variable expressivity within families suggests that other genes or environmental factors are involved in the causal pathway leading to a particular epilepsy phenotype. Further, in three of the four genes found to be mutated in GEFS+ families, mutations have been identified in other syndromes also: SCN1A mutations (many of which are de novo) in patients with SMEI,19,69,110,124 SCN2A mutations in families with benign familial neonatal infantile seizures,43 and GABRG2 mutations in families with childhood absence epilepsy with febrile seizures.50,125 Again, this variable expression across families probably reflects the involvement of other genes or environmental factors in the phenotypes under study, although variation in the types of mutations in the gene involved may also play a role.
Finally, the effects of some genotypes on epilepsy may involve gene–environment interaction, that is, the joint influence of genetic and environmental factors in a causal pathway leading to disease.71,72,95 Gene–environment interaction might explain some of the reduced penetrance observed in the epilepsy genes discovered so far. For example, some genotypes might not affect risk directly, but instead might increase susceptibility to the effects of environmental factors. In this case, individuals who inherit the risk-raising genotype would not develop epilepsy unless they were also exposed to the environmental factor; hence, some susceptibility genes might contribute to remote symptomatic epilepsy and even to acute symptomatic seizures as well. In a study by Schaumann et al.,98 seizure risk was increased in the relatives of people who had seizures associated with heavy alcohol consumption (either unprovoked seizures associated with chronic alcohol abuse or acute symptomatic seizures associated with alcohol intoxication), suggesting that some genotypes may interact with alcohol exposure to raise risk. In the same study, however, risk was not increased in the relatives of people with posttraumatic epilepsy.
Research Approaches in Genetic Epidemiology
In the study of a complex disorder such as epilepsy, genetic epidemiologists use a series of study designs to elucidate the genetic contributions on the population, family, and molecular levels. These studies begin with the assessment of familial aggregation: To what extent is the risk of epilepsy (or other disorders) increased in the relatives of people with epilepsy? Evidence of familial aggregation has only limited utility in evaluating genetic hypotheses; significant familial clustering can arise from shared environmental exposures (e.g., air pollutants) or high-risk behavior practices (such as diet) in members of the same family, in addition to genetic factors. Thus, the next step is to use special designs such as twin studies or adoption studies to ask: To what extent is the familial aggregation due to shared genes as opposed to shared environment? If a significant genetic effect is observed, additional studies must be carried out to determine what types of genetic effects underlie susceptibility. At one extreme, the genetic effects could involve single genes with a major effect on susceptibility, whether autosomal or X-linked, dominant or recessive. At the opposite extreme, some genetic influences could be polygenic; that is, they could be a consequence of the effects of a large number of genes at different loci, each of which individually contributes only slightly to the risk. Between these two extremes, some influences might involve pairs or small groups of genes, possibly with interactive (epistatic) effects. One method that can be used to distinguish among these possibilities, segregation analysis, involves examining the distribution of disease occurrence in families and testing its consistency with various mendelian models (autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive, X-linked dominant). This method has been used in only a few studies of human epilepsies.34,47,68,81,92 Finally, studies must be designed to investigate the molecular mechanisms by which the genes influence risk. At this stage, the specific genes involved need to be identified, and their basic pathophysiologic effects studied. So far, most studies aimed at gene identification have employed linkage analysis and subsequent positional cloning; many newer studies are using allelic association designs. Below we review these approaches and what has been learned from each in genetic studies of the epilepsies.
Collection of Family History Data
Accurate information about seizure occurrence in family members is essential for almost all designs used to test genetic hypotheses about epilepsy and other seizure disorders. In most genetic studies of epilepsy, data are obtained indirectly, in “family history” interviews in which the proband with epilepsy (or a parent or other caregiver, if the proband is a child) is interviewed about seizures in other family members. For many disorders, family history data obtained in this way have low sensitivity—many truly affected relatives are misclassified as unaffected. This problem can usually be remedied by using a “family study” design, in which each relative is examined or given a diagnostic interview directly. Study of the genetic epidemiology of epilepsy presents a unique problem, however, because the diagnosis in both probands and relatives cannot usually be made on the basis of physical examination or laboratory testing. It is essentially historical, based on a description of seizure events that occurred prior to visiting the physician.
Ottman et al. evaluated the validity of family history data on parents and siblings, collected in semistructured family history interviews with adults with epilepsy.83 In this study, many of the parents and siblings of these subjects were also interviewed about their own seizure histories and those of their other family members. The relatives’ self-reports or their mother’s reports were used as the “gold standard” in deciding whether or not they had seizure disorders. The results suggested that adults with epilepsy can report reasonably accurately about epilepsy in their parents and siblings, but isolated unprovoked seizures and acute symptomatic seizures are underreported. Sensitivity for epilepsy (i.e., the proportion of relatives with epilepsy who were correctly reported to have had seizures in the family history interview) was 87% assuming the mother’s report was correct, and 93% assuming the self-report was correct. For other seizure disorders in relatives, sensitivity was only 32% assuming the mother’s report was correct, and 18% assuming the self-report was correct.
Evidence also suggests that family history information on epilepsy is less accurate for older relatives than for younger relatives. One study based on family history reports found an apparent “cohort effect” in the familial risks for epilepsy, with a 50% increase in the proportion of relatives reported to be affected, for each 20-year increase in birth year of the relatives.85 This effect could not be attributed to a real change in risk over time, because the age-specific incidence rates of epilepsy among persons younger than 40 years did not increase during the time periods investigated.42 Instead, the apparent cohort effect was probably an artifact of better recall of recent events than of past events. In the older relatives, a diagnosis of childhood onset epilepsy would have occurred many years before the family history interviews were done, whereas in the younger relatives such a diagnosis would have occurred more recently. Thus, the subjects who were interviewed about their family histories were probably less likely to remember (or even to know
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about) epilepsy in their older relatives than in their younger relatives.
Familial Aggregation Studies
Most early studies of the genetics of epilepsy were devoted to assessing familial aggregation, that is, an increased risk for epilepsy in the relatives of affected persons compared with risks in the general population (or relatives of unaffected persons). In familial aggregation studies a sample of people with epilepsy (probands) is ascertained, and then the risk of epilepsy is examined in the relatives of the probands and compared with the risk in the population or in the relatives of controls without epilepsy. The probands may also be divided into subsets based on syndromes or other clinical features (etiology, age at onset, seizure type, etc.), and the risks in the relatives of the different subsets compared. Also, the risks of specific clinically defined subsets of epilepsy (or other disorders) may be examined in the relatives and compared with the risks of the same outcomes in the relatives of controls (or the general population).
Several problems of epidemiologic design and analysis have impeded progress in these studies. Many studies used highly selected populations, possibly introducing bias in the estimates of the magnitude of increased risk. Few studies used comparison groups, rigorous methods for obtaining information about family history, or standardized interview methods. Many studies failed to specify which classes of relatives were included. In the analysis of risks in relatives, age adjustments were seldom made. Definitions of epilepsy were often ambiguous. The outcome of interest in the relatives was seldom clearly defined. Some studies defined only those with epilepsy as affected, whereas others included those with any type of seizure disorder or those with only electroencephalogram (EEG) abnormalities.
The best estimates of familial aggregation are derived from the work of Annegers et al., using population-based data from the Rochester Epidemiology Project.3,5,6,7,76,77,78 The Rochester Epidemiology Project is a unique exception to the usual methods used in familial aggregation studies of the epilepsies and other disorders. It takes advantage of the records linkage system of the Mayo Clinic, which includes essentially all medical, surgical, and pathologic diagnoses of residents of Olmsted County from 1922 to the present, and therefore provides an excellent resource for epidemiologic studies of epilepsy and other disorders.8,59 This system was adapted for collection of genetic information using a three-step procedure that avoids the use of interviews completely. First, probands with epilepsy were identified by searching the records of the Mayo Clinic to identify all children aged younger than 16 years with diagnoses of idiopathic or cryptogenic epilepsy or isolated unprovoked seizures while residing in Rochester after 1935. Second, the records were used to identify the parents of these probands, and all of the other descendants of the parents (i.e., the probands’ siblings, children, nieces and nephews, and grandnieces and grandnephews). Third, the medical records of these relatives at the Mayo Clinic and all other medical facilities serving southeastern Minnesota were reviewed for evidence of seizure dis-orders.
This study design offers several unique advantages for genetic studies. The problem of selection bias is avoided because all incident cases of epilepsy during a specified time period were included; the data on seizure disorders in relatives have high validity, because they are obtained by careful, page-by-page review of the relatives’ medical records rather than by proband interviews; and the clinical detail on both probands and relatives is extensive. This approach would be impossible in most studies, because family members often live in different areas and access to their medical records is very difficult to obtain.80 The only major disadvantages are the limitation in sample size imposed by the relatively small population of Rochester and the restriction to probands with childhood onset, idiopathic or cryptogenic epilepsies, which limited some of the comparisons that could be done in the analysis.
In the Annegers et al. study, the cumulative incidence of epilepsy to age 20 years was 3.6% in siblings and 10.6% in offspring of probands with idiopathic or cryptogenic epilepsy beginning before age 16, compared with 1.7% in the Rochester population.4 The standardized incidence ratios (SIRs) for epilepsy in the relatives of individuals with idiopathic or cryptogenic, childhood-onset epilepsy were 2.5 (95% confidence interval [CI], 1.3 to 4.4) in siblings and 6.7 (95% CI, 1.8 to 17.1) in offspring.5 Risk for unprovoked seizures was not increased in more distant relatives (e.g., nieces and nephews or grandchildren). In a later study of the same population with additional live births and follow-up, Ottman et al.76 found that the SIR for offspring was lower than in the Annegers et al. study: 3.4 (95% CI, 2.1 to 5.1). The lower risks in the more recent study were partly due to a larger number of offspring, leading to greater precision in the risk estimates than in the earlier study. Another possible explanation relates to a difference in study design: The probands in the Annegers et al. study were restricted to incident idiopathic or cryptogenic epilepsy cases with onset prior to age 16, whereas those in the Ottman et al. study were all prevalent epilepsy cases during a specified time period (regardless of etiology or age at onset).
Table 2 Risk of Epilepsy in Siblings, by Etiology of Epilepsy in the Probanda
  Classification of epilepsy in probands
  Idiopathic or cryptogenic Symptomatic
Harvald39 4.2 1.2
Eisner et al.28,b 5.5  
Annegers et al.4,b 2.7  
Ottman et al.79 2.4 0.8
aCumulative incidence to age 20 reported in all studies except Harvald.
bRestricted to siblings of probands with onset prior to age 16.
Familial aggregation studies can provide important information about etiologic and genetic heterogeneity. Comparisons of probands with different epilepsy syndromes or other clinical characteristics, in terms of the risks for seizure disorders in close relatives, have indicated which subgroups are most strongly influenced by a genetic susceptibility. One of the most consistent findings has been that relatives of patients with idiopathic or cryptogenic epilepsy have a higher risk than relatives of those with remote symptomatic epilepsy.2,39,56,79,86,120 Table 2 shows the results of four studies that reported sibling risks of epilepsy, stratified by the etiology of epilepsy in the probands. Risks to age 20 years ranged from 2% to 5% in the siblings of probands with idiopathic or cryptogenic epilepsy. However, two studies that examined risks in siblings of probands with symptomatic epilepsy found risks of approximately 1%, which is not higher than in the general population. This lack of increased risk in the relatives of probands with symptomatic epilepsies suggests that genetic influences are relatively minor in most symptomatic epilepsies (caused by traumatic brain injury, stroke, brain infection, etc.). On the other hand, genes that raise susceptibility to the effects of specific types of brain insults may play a role in some symptomatic cases. If this is true, then in the families of these symptomatic probands, an increased risk would be
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expected only in the relatives who were exposed to the same types of brain insults as the probands. Since these exposures are likely to be uncommon, the risk in their relatives overall (without taking into account which are exposed) is unlikely to be increased.
Risk of epilepsy has also been found to be higher in the relatives of probands with earlier age at onset of epilepsy than in the relatives of those with later onset.2,28,56,79,86 Lennox56 reported a gradient of risk in first-degree relatives with proband age at onset. Risks were highest in relatives of probands with onset before 5 years of age, intermediate in relatives of probands with onset between 5 and 19 years of age, and lowest in relatives of probands with older ages at onset. In the Minnesota Clinical Epilepsy Research Program,2 sibling risks were higher for probands with age of onset at 25 years or less than for those with later ages of onset. Eisner et al.28 found the highest risks in first-degree relatives of probands with onset before 4 years of age. Ottman et al. also found a higher risk in the relatives of probands with earlier age at onset.79,86 Moreover, they found that the degree of increased risk diminished with increasing age of the relatives; among relatives who reached age 35 without developing epilepsy, risk was not increased.79
Another important finding is that risks are higher in the remaining relatives of probands with a family history than in the relatives of those without a family history.51,60,81 In one study, the siblings of probands with IGE had a 4% risk of idiopathic or cryptogenic epilepsy overall, but a much higher risk if they also had an affected parent (15%) or another affected sibling (22%) in addition to the proband.81 In the same study, the siblings of probands with cryptogenic localization-related epilepsy had a 2% risk of idiopathic or cryptogenic epilepsy overall, but a 3% risk if a parent was affected and a 10% risk if another sibling was affected.81
It is widely assumed that risk is higher in the relatives of patients with generalized epilepsy than in relatives of those with localization-related epilepsy, but in most studies the difference between these two groups is small.73,74 In analyses of offspring of epilepsy patients in Rochester, Minnesota,77 the higher risk in offspring of parents with generalized seizures was entirely attributable to very high risks in offspring of the subset with absence seizures. Thus, for the majority of patients with generalized seizures, risk in offspring was no higher than in the offspring of patients with partial seizures.
In understanding the relations between genotype and phenotype in the epilepsies, two alternative models can be envisioned.128,130 The first model postulates that different sets of genes influence risk for different epilepsy syndromes (“distinct genetic influences”), and the second, that the same genes influence risk for different epilepsy syndromes (“shared genetic influences”). Familial aggregation studies can be used to distinguish between these possibilities by investigating whether, in the families of probands with specific types of epilepsy, risk is increased only for the same types as in the probands or for all types of epilepsy. If the genetic influences on different types of epilepsy are distinct, then among the relatives of probands with a given type, risk will be increased only for the same type as in the proband. On the other hand, if the genetic influences on different types of epilepsy are shared, risk in the relatives will be increased for all types, including those different from that in the proband. In two studies that used this approach, evidence was obtained for shared genetic influences on generalized and localization-related epilepsy. In the relatives of probands with generalized epilepsy, risk for localization-related epilepsy was significantly increased (fourfold), both in population-based data from Rochester, Minnesota,77 and data from the Epilepsy Family Study of Columbia University.84
However, other studies suggest that clinical characteristics of epilepsy tend to cluster in families. Both Tsuboi119 and Beck-Mannagetta et al.11 found that the distribution of seizure types in affected relatives was skewed toward the same types of seizures as in the probands, although different seizure types were also seen. In a study of 72 families of probands with idiopathic generalized epilepsies, each of which contained more than three affected individuals, multiple idiopathic generalized epilepsies were seen in 75% of families, but there were very few cases of localization-related epilepsy.1 These findings are difficult to interpret because they do not take into account what distribution of syndromes would be expected in the families by chance alone.
Winawer et al. developed a method based on permutation testing to test hypotheses about shared and distinct genetic influences on different clinically defined subsets of epilepsy.128,129,130,131 The method, family concordance analysis, assesses the concordance of epilepsy types (syndromes, seizure types, or subsets defined by other clinical features) in families containing multiple affected individuals. The rationale for the analysis is that if some of the genetic influences on different epilepsy types are distinct, families will tend to be concordant—that is, the proportion of families in which all affected individuals have the same type of epilepsy will exceed that expected by chance. The results of studies using this approach have provided evidence for distinct genetic influences on generalized and localization-related epilepsy.130 Within the IGEs, these studies found evidence for distinct genetic influences on different seizure types: Myoclonic, absence, and generalized tonic–clonic.129,131 With respect to different syndromes within the IGEs, they found evidence for distinct genetic influences on JME versus the two absence epilepsy syndromes (childhood absence epilepsy [CAE] and juvenile absence epilepsy [JAE] combined), but not for distinct influences on CAE versus JAE.129,131
There is a strong basis for assuming a common genetic basis for epilepsy and febrile seizures. Hauser et al.41 found that risk for epilepsy is increased to the same extent in relatives of probands with febrile seizures as in relatives of probands with epilepsy. However, when the proband had both epilepsy and febrile seizures, risk for epilepsy was increased to a greater extent, suggesting that a higher genetic liability is required to manifest both disorders. These results parallel those from recent studies of GEFS+, in which the identified genes raise risk for both epilepsy and febrile seizures.9
The findings of three previous studies suggest the possibility of a shared genetic susceptibility to epilepsy and cerebral palsy. In the National Collaborative Perinatal Project, incidence of cerebral palsy in offspring was associated with the mother’s history of epilepsy67; and incidence of nonfebrile seizure disorders in offspring without cerebral palsy was associated with a history of motor deficits in siblings.66 Similarly, Rimoin and Metrakos93 reported an increased prevalence of convulsions and epileptiform EEG abnormalities in relatives of children with hemiplegia, a specific form of cerebral palsy. Finally, Ottman et al. found an increased risk of idiopathic or cryptogenic epilepsy in the first-degree relatives of probands with epilepsy associated with neurologic deficits presumed present at birth (many of whom had cerebral palsy), although the numbers were too small to reach statistical significance.79
Table 3 Percent of Offspring with Epilepsy, by Sex of Affected Parent
Authors % of offspring with epilepsy, among
Offspring of mothers with epilepsy Offspring of fathers with epilepsy
Tsuboi and Endo120 2.9 1.7
Janz and Beck-Mannagetta46 4.0 2.7
Ottman et al.76 8.7a 2.4a
aCumulative incidence of epilepsy to age 25 in offspring.
An intriguing aspect of the familial distribution of epilepsy pertains to the risks in offspring: Risks of epilepsy and febrile seizures are higher in the offspring of affected women than in the offspring of affected men (Table 3).7,46,76,82,120 This maternal effect has been observed consistently in previous studies, and is not compatible with any conventional genetic model.75,82 In population-based data from Rochester, the risk of epilepsy by age 25 years was 8.7% in offspring of affected women and 2.4% in offspring of affected men, compared with 1.6% in the Rochester population.76 Additional analyses indicated that this difference could not be explained by intrauterine exposure to seizures or anticonvulsants in offspring of women with epilepsy, or patterns of selective fertility that might lead to a
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higher proportion of affected mothers than affected fathers with familial forms of epilepsy.76,101,102,103 An increased frequency of some complications of pregnancy and delivery has been reported in women with epilepsy, but these complications are not associated with increased risk for seizures in their offspring113 and thus could not explain the higher seizure risk in offspring of women than of men with epilepsy. The possible roles of mitochondrial genes, imprinted nuclear genes, or expanded repeat mutations remain to be investigated.
Twin Studies
Studies of twins are ideal for disentangling genetic from nongenetic causes of familial aggregation. For this purpose, the within-pair similarities (or concordance rates) of monozygotic (MZ) and dizygotic (DZ) twins are compared, on the assumption that genetic effects would produce greater similarity in the two co-twins of a monozygotic pair (who share 100% of their genes) than in the two co-twins of a dizygotic pair (who share 50% of their genes on average).
Concordance rates for epilepsy are consistently higher in monozygotic twins than in dizygotic twins13,20,45,52,53,55,57,105,121 (Table 4), although the concordance rates vary across studies because of differences in methodology such as twin ascertainment methods, numbers of pairs included, approaches for diagnosis and classification, and methods used to calculate concordance. In the classic twin study by Lennox,55 concordance rates were higher in MZ than DZ pairs only for twins with “intact brains,” illustrating the greater importance of genetic factors in idiopathic or cryptogenic epilepsies than in symptomatic epilepsies.
Table 4 Concordance Rates of Epilepsy in Monozygotic and Dizygotic Twins
Authors (reference) Concordance rate (%)
Monozygotic twins Dizygotic twins
Lennox55    
   Brain injured 11 7
   Intact 70 6
Inouye45 54 7
Corey et al.20 19 7
Silanpaa et al.105 10 5
Berkovic et al.13    
   Generalized epilepsy 82 26
   Localization-related epilepsy 36 5
Kjeldsen et al.52    
   Generalized epilepsy 65 12
   Localization-related epilepsy 30 10
Vadlamudi et al.52,a    
   Generalized epilepsy 80 27
   Localization-related epilepsy 9 6
aReanalysis of data from Lennox.56
More recently, twin studies have been used to investigate the shared and distinct genetic influences on different types of epilepsy and to provide evidence for distinct genetic effects on generalized and localization-related epilepsies. In a study of 253 Australian twin pairs, Berkovic et al.13 found evidence not only for the genetic influences on epilepsy as a whole, but also for specific epilepsy subtypes. For example, MZ concordance rates were higher than DZ concordance rates in analyses restricted to either generalized epilepsy or localization-related epilepsy (Table 4). Among MZ twin pairs concordant for epilepsy, 94% had the same International League against Epilepsy (ILAE) major epilepsy syndrome compared with 71% of DZ twin pairs with epilepsy. Re-examination of Lennox’s twin data with classification of seizure types and syndromes by modern ILAE criteria confirmed these findings: 86% of MZ pairs and 60% of DZ pairs were concordant for ILAE syndrome.121 The results were very similar in another recent population-based twin study.52 Concordance rates were higher in MZ than in DZ pairs not only for epilepsy overall, but also for generalized epilepsy and localization-related epilepsy specifically (Table 4); and among pairs concordant for epilepsy, 83% of MZ pairs and 65% of DZ pairs were concordant for syndrome. These findings are consistent with those from the family concordance study of Winawer et al.130 but differ from those in the familial aggregation studies, in which the risks for localization-related epilepsy were elevated in the families of probands with generalized epilepsy.77,84 One possible explanation is that some genetic influences on generalized and localization-related epilepsies are distinct and others shared, and the different study designs vary in their ability to detect these different influences.
Linkage Analysis
Linkage analysis is a powerful tool used to localize, or map, a gene to a small chromosomal region. This is a first step in positional cloning, in which a disease-related gene is identified from among the 20,000 to 30,000 genes in the human genome by first narrowing the search to a small number of genes in a specific chromosomal region, and then examining the nucleotide sequence of the genes in that region to identify a mutation that is likely to affect disease risk. The basic approach to linkage analysis is an investigation of the co-inheritance of genes or disease with genetic marker alleles within families. The closer two genes are on a chromosome, the less likely they are to be separated by recombination; hence, the alleles of genes located close together are inherited together more often than expected by chance. The direct linear relationship between number of recombination events and the distance between genes is at the root of genetic linkage analysis. The statistic used to assess the evidence for linkage is the lod score, defined as the log10 of the ratio of two probabilities: The probability that the family
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data would be observed under the hypothesis of linkage at a specific recombination fraction (numerator) and the probability that the data would be observed under the hypothesis of no linkage (denominator). In a genome-wide analysis, a lod score of 3.0 is generally accepted as significant evidence for linkage at p <0.05.
Many linkage findings have been reported in various epilepsy syndromes or subsets. Some, but not all, of these have led to the identification of mutations in risk-raising genes, and some of the published findings will probably turn out to be false positives. The linkage findings are too numerous to list all of them here, but some of the most important and consistent results are summarized below.
An intense effort has been made to identify linkage in the IGE syndromes, which show strong familial aggregation and usually nonmendelian inheritance (although mendelian forms of IGE have also been described, and three genes listed in Table 1, CLCN2,40 GABRA1,21 and EFHC1,114 were identified in these forms). In the genetically complex IGEs, evidence has been reported for linkage to a wide array of chromosomal regions, including 2q36,97 3q26,97 5p,25 6p21,21,26,34,89,96,117,127 6p12,21,114 8p12,25,27 13q31,117 14q23,97 15q14,29 and 18q12.25 The most consistent result is linkage to the HLA region (chromosome 6p21); many of the other linkage findings have been inconsistent across groups.
One particularly promising linkage finding at present is in familial partial epilepsy with variable foci, a syndrome first described in a family with complex partial and secondarily generalized, primarily nocturnal seizures.99 Interictal EEGs in affected family members revealed frontal, temporal, and occasionally occipital epileptic foci.99,132 Linkage to chromosome 22q11 has been reported in three large families with this syndrome.14,16,132 The gene has not yet been identified, but the minimal genetic region has been narrowed to a 5.2 megabase region on chromosome 22. Identification of a gene that raises risk for this syndrome could provide interesting information about the heritable mechanisms underlying multifocal pathology.
A number of studies have used linkage analysis to localize genes for febrile seizures, but these findings have not led to gene discoveries so far. In studies of large families with apparently autosomal dominant inheritance, evidence was found for linkage to four chromosomal regions: FEB1 on chromosome 8q13-21,123 FEB2 on chromosome 19p13,48,54 FEB3 on chromosome 2q23-24,90 and FEB5 on chromosome 6q22-24.64 In a series of 47 small families, another study found evidence for linkage to another region, FEB4 on chromosome 5q14-15.65 One of the challenges in these studies is distinguishing the different phenotypes of febrile seizures. In many of the reported families, it is unclear whether the phenotype should be called isolated febrile seizures or GEFS+ (involving febrile seizures persisting to late ages or accompanied by afebrile generalized tonic–clonic seizures), and no standardized criteria for GEFS+ are available to help resolve this problem. For example, some investigators suggested that the family in which the FEB3 locus was reported on chromosome 2q23-24 actually had GEFS+, so the locus should not have been named FEB3.63,100
Allelic Association Studies
In epilepsy as in other disorders, allelic association studies are now being used as an alternative to positional cloning for the detection of disease genes.116 These studies are aimed at detecting genetic variants that are more common in people with epilepsy than in unaffected persons from the same population. A significantly increased frequency of a variant in people with epilepsy would suggest either that it directly affects risk for epilepsy, or that it is located very close to a functional variant on the same chromosome, and very often inherited with the functional variant (linkage disequilibrium). The genetic variants examined are usually single nucleotide polymorphisms (SNPs), common DNA sequence variations where one of the four nucleotides is substituted for another, found every 1,000 to 2,000 nucleotides in the human genome and accounting for about 90% of all DNA polymorphisms. Most allelic association studies have focused on variants in candidate genes with a hypothesized effect on disease risk (such as genes encoding ion channels). Recently, however, investigators have begun to undertake genome-wide association studies, and this approach will be used in the epilepsies soon.17,44
Allelic association studies have important advantages for the study of complex diseases. Unlike linkage studies, they do not require families with multiple affected individuals, which are so rare in the epilepsies. Also, they have greater statistical power than linkage studies for the detection of genes with a small effect on disease risk.94
Allelic association studies also have potential limitations. The validity of their basic underlying assumption—that nonmendelian epilepsies result from DNA variations common to a relatively large proportion of cases (the so-called “common disease-common variant hypothesis”)37—is still unknown. If many different combinations of risk-raising variants in multiple genes produce similar epilepsy phenotypes, none of the variants may be common enough to be detected through allelic association. Also, the contributions of somatic mutations and de novo mutations to complex epilepsies are unknown.
The potential for population stratification, a special type of confounding, must be considered in the design and interpretation of allelic association studies. It arises when the cases and controls in a study have different genetic ancestries and the ancestral groups differ in their allelic distributions. As a result, the cases and controls could differ in the frequency of an SNP of interest for reasons unrelated to the disease. The magnitude of the effect of stratification on current allelic association studies is controversial.118,122 but fortunately, a number of methods have been developed to control for its effects, including family-based association tests,133 genomic control,23 and structured association tests.91
In the epilepsies, a large number of candidate gene-based allelic association studies have been published, and the pace of publication has increased dramatically in recent years (reviewed in reference 116). Many of the published studies have been plagued by methodologic limitations such as small sample size, lack of control for population stratification, and failure to adjust for multiple statistical tests. Few genetic variants have been examined in more than a single study, and among those that have, few of the reported associations have been replicated.88,116 Thus, although clearly this approach holds great potential, we are still in the earliest stages of its application in the epilepsies.
Another approach, combining linkage and association analysis, has been used in the IGEs with promising results. A genome scan of 91 families with genetically complex adolescent-onset IGEs provided evidence for a locus common to most IGEs on chromosome 18q21, a locus on chromosome 6p21 for JME, and other loci (on chromosomes 8 and 5) influencing risk for other forms of IGEs.25 The authors suggested that interactions of different combinations of these genes produce the varied phenotypes found in IGE families. In subsequent association studies in the same set of families, they found an association of JME with two SNPs in the promoter region of the BRD2 (RING3) gene on chromosome 6, suggesting that this might be the chromosome 6p21-linked JME gene, although no causative mutations were identified.89 They also found evidence for association of IGEs with a haplotype of SNPs within the malic enzyme 2 gene on chromosome 18, suggesting that this might be the chromosome 18-linked gene predisposing to
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IGE33; however, a subsequent study by other authors failed to confirm this finding.58
Studies in pharmacogenomics use allelic association designs to attempt to identify genetic variations related to antiepileptic drug response or toxicity. This is a rapidly expanding research area that may transform the use of anticonvulsants as well as other medications.31 The polymorphisms examined are usually in genes coding for drug-metabolizing enzymes, receptors, and transporters. Understanding the genetic influences on individual variability in drug response may someday help health care practitioners identify patients at risk of toxicity from certain medications, adjust doses based on genetically determined rates of drug metabolism, and select appropriate medications for patients based on their metabolic profile.
Summary and Conclusions
Research in the genetic epidemiology of the epilepsies is advancing very rapidly; a number of genes that influence risk for mendelian forms of epilepsy have already been identified, and efforts to identify others are continuing. Despite the importance of these gene discoveries, however, they apply to only a small minority of patients. Research to elucidate the genetic influences in the remaining patients—most of whom have no affected relatives—is one of the most challenging and exciting prospects for the near future. Current evidence indicates that the genetic mechanisms that contribute to risk vary across some clinically defined subgroups of epilepsy. Genetic mechanisms also vary across families, even within narrowly defined clinical subsets or syndromes. Environmental factors may also contribute to susceptibility, even in the presence of genetic influences. Further research on the mechanisms by which genes influence risk is extremely important. It could transform clinical management of the epilepsies, leading the way to the development of new therapies and perhaps even ways to prevent epileptogenesis in the future.
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