Recent Advances in the Molecular Genetics of Epilepsy
Recent Advances in the Molecular Genetics of Epilepsy
Epilepsy is a common disorder with a prevalence of 4–8 per 1000 in Western countries and a lifetime cumulative incidence of about 3%. In approximately 20%–30% of cases there is a clear extraneous acquired cause (eg, head trauma, stroke) but in the remainder genetic factors have a major role. The evidence for this is a twofold to fourfold increase in risk in first degree relatives and heritability estimates of around 70% derived from twin studies of epilepsies without known cause.
During the last 15 years, major achievements have been made in detecting new Mendelian epilepsy genes. Positional cloning of rare multi-generational autosomal dominant families has identified a number of genes definitively associated with epilepsies including ion channel subunits (CHRNA4, CHRNA2, CHRNB2, GABRG2, GABRA1, KCNQ2, KCNQ3, SCN1B, SCN1A, SCN2A) but also non-ion channel genes (ARX, CDKL5, LGI1, PCDH19, SLC2A1, SPTAN1, STXBP1) ( Table 1 ).
These advances in monogenic epilepsies have been accompanied by an exponential increase in our understanding of the contribution of susceptibility alleles, de novo mutations and copy number variants (CNVs) to epilepsy pathogenesis through studies of families and sporadic patients, as outlined in the next section of this review. Despite this, determining genetic contributions to common epilepsies remains challenging. There is strong evidence that these have complex inheritance—that is determined by multiple genes (polygenic) with or without environmental influences (figure 1). This evidence includes clinical genetic data of recurrence risks in relatives, coupled with twin and family analyses (reviewed in ).
(Enlarge Image)
Figure 1.
Contributions to common epilepsies. The causation of common epilepsies is a biological continuum due to the overlap between genetic and acquired cases. The vertical axis represents approximate frequency. Among genetic epilepsies polygenic cases are predominant and the vast majority remain unsolved. Adapted from [5].
The notable research advances in monogenic epilepsies have not yet translated into widespread utilisation in the clinic. This translational gap between research discoveries and clinical practice reflects the fact that diagnostic tests are still performed using classical sequencing technology based on the Sanger method and are often expensive and inaccessible. These automatic DNA sequencers are very useful but are limited by slow throughput, which makes extensive sequencing of all known epilepsy genes expensive and time consuming. For this reason, even in major centres, only a very small number of genes are screened for mutations, and as a result, in a large percentage of persons with epilepsy a potentially diagnosable genetic cause is not recognised.
The limitations of traditional sequencers, and the genetic heterogeneity and phenotypic variability associated with epilepsy, highlight the need for new DNA sequencing technologies to allow complete screening of all known and clinically appropriate epilepsy genes in a quick and cost-effective way. Although large scale screening platforms exist for other heterogeneous genetic diseases, including a DNA resequencing microarray for deafness ('OtoChip'), no such platform currently exists for epilepsy.
More promising for the epilepsies are massively parallel sequencing technologies (MPS) that have recently emerged, including the 454 GS FLX (Roche), Solexa (Illumina) and SOLiD (Applied Biosystems) sequencing systems. These methods offer exceptionally high-throughput with high accuracy and potentially cheaper analyses. Proof-of-principle MPS platforms have been developed for hearing loss, ocular diseases and breast cancer. These platforms have been optimised for DNA diagnostics, which has specific requirements including: (1) high-throughput screening of selected regions; (2) high sensitivity to detect all types of mutations (all sequencing mutations and large rearrangements); (3) the need for only small amounts of sample material; (4) high reliability; and (5) cost-effectiveness. Very recently, MPS technology has been applied to clinical diagnostic screening of known epilepsy genes and identification of novel epilepsy genes, as outlined in the section 'Recent advances in the molecular genetics of epilepsy: MPS for gene discovery' of this review. Based on these promising results, comprehensive clinical testing for epilepsy will soon become widely available to patients in the clinic.
Nonetheless, the perceived slow translation of genetic knowledge to the clinic has led to some misconceptions concerning the importance of genetic factors in epilepsy pathogenesis. In turn this has promoted a clinical underascertainment bias for genetic aetiologies. This is compounded by increasing evidence for the role of de novo mutagenesis in epilepsies where, in such cases, family history, much less Mendelian segregation, is usually lacking. A further issue is the economics of offering genetic testing. Most Mendelian disorders including many epilepsies are rare, making them unattractive for commercialisation and, in addition, the testing of some genes is protected by patents. A low propensity to consider a genetic aetiology and delayed diagnoses also stifle advances in commercial genetic testing services and therapeutics. The reality for many public healthcare providers is that it is difficult to obtain funding for single gene testing despite established correlations between genotype and therapeutic protocols; for example, the ketogenic diet in patients diagnosed with GLUT1 deficiency. A serious cost–benefit analysis of comprehensive genetic testing for epilepsy has not been conducted; however, it is likely that earlier genetic diagnosis would significantly reduce the economic burden of repeat hospitalisations associated with unnecessary investigations, and seizure exacerbation due to the inappropriate choice of antiepileptic drugs that may occur without an accurate diagnosis. We begin with a discussion of advances in understanding genetic epilepsies, beyond the classical Mendelian disorders, which are reviewed elsewhere, and then analyse recent clinical and research discoveries in epilepsy facilitated by MPS.
Introduction to the Molecular Genetics of Epilepsy
Epilepsy is a common disorder with a prevalence of 4–8 per 1000 in Western countries and a lifetime cumulative incidence of about 3%. In approximately 20%–30% of cases there is a clear extraneous acquired cause (eg, head trauma, stroke) but in the remainder genetic factors have a major role. The evidence for this is a twofold to fourfold increase in risk in first degree relatives and heritability estimates of around 70% derived from twin studies of epilepsies without known cause.
During the last 15 years, major achievements have been made in detecting new Mendelian epilepsy genes. Positional cloning of rare multi-generational autosomal dominant families has identified a number of genes definitively associated with epilepsies including ion channel subunits (CHRNA4, CHRNA2, CHRNB2, GABRG2, GABRA1, KCNQ2, KCNQ3, SCN1B, SCN1A, SCN2A) but also non-ion channel genes (ARX, CDKL5, LGI1, PCDH19, SLC2A1, SPTAN1, STXBP1) ( Table 1 ).
These advances in monogenic epilepsies have been accompanied by an exponential increase in our understanding of the contribution of susceptibility alleles, de novo mutations and copy number variants (CNVs) to epilepsy pathogenesis through studies of families and sporadic patients, as outlined in the next section of this review. Despite this, determining genetic contributions to common epilepsies remains challenging. There is strong evidence that these have complex inheritance—that is determined by multiple genes (polygenic) with or without environmental influences (figure 1). This evidence includes clinical genetic data of recurrence risks in relatives, coupled with twin and family analyses (reviewed in ).
(Enlarge Image)
Figure 1.
Contributions to common epilepsies. The causation of common epilepsies is a biological continuum due to the overlap between genetic and acquired cases. The vertical axis represents approximate frequency. Among genetic epilepsies polygenic cases are predominant and the vast majority remain unsolved. Adapted from [5].
The notable research advances in monogenic epilepsies have not yet translated into widespread utilisation in the clinic. This translational gap between research discoveries and clinical practice reflects the fact that diagnostic tests are still performed using classical sequencing technology based on the Sanger method and are often expensive and inaccessible. These automatic DNA sequencers are very useful but are limited by slow throughput, which makes extensive sequencing of all known epilepsy genes expensive and time consuming. For this reason, even in major centres, only a very small number of genes are screened for mutations, and as a result, in a large percentage of persons with epilepsy a potentially diagnosable genetic cause is not recognised.
The limitations of traditional sequencers, and the genetic heterogeneity and phenotypic variability associated with epilepsy, highlight the need for new DNA sequencing technologies to allow complete screening of all known and clinically appropriate epilepsy genes in a quick and cost-effective way. Although large scale screening platforms exist for other heterogeneous genetic diseases, including a DNA resequencing microarray for deafness ('OtoChip'), no such platform currently exists for epilepsy.
More promising for the epilepsies are massively parallel sequencing technologies (MPS) that have recently emerged, including the 454 GS FLX (Roche), Solexa (Illumina) and SOLiD (Applied Biosystems) sequencing systems. These methods offer exceptionally high-throughput with high accuracy and potentially cheaper analyses. Proof-of-principle MPS platforms have been developed for hearing loss, ocular diseases and breast cancer. These platforms have been optimised for DNA diagnostics, which has specific requirements including: (1) high-throughput screening of selected regions; (2) high sensitivity to detect all types of mutations (all sequencing mutations and large rearrangements); (3) the need for only small amounts of sample material; (4) high reliability; and (5) cost-effectiveness. Very recently, MPS technology has been applied to clinical diagnostic screening of known epilepsy genes and identification of novel epilepsy genes, as outlined in the section 'Recent advances in the molecular genetics of epilepsy: MPS for gene discovery' of this review. Based on these promising results, comprehensive clinical testing for epilepsy will soon become widely available to patients in the clinic.
Nonetheless, the perceived slow translation of genetic knowledge to the clinic has led to some misconceptions concerning the importance of genetic factors in epilepsy pathogenesis. In turn this has promoted a clinical underascertainment bias for genetic aetiologies. This is compounded by increasing evidence for the role of de novo mutagenesis in epilepsies where, in such cases, family history, much less Mendelian segregation, is usually lacking. A further issue is the economics of offering genetic testing. Most Mendelian disorders including many epilepsies are rare, making them unattractive for commercialisation and, in addition, the testing of some genes is protected by patents. A low propensity to consider a genetic aetiology and delayed diagnoses also stifle advances in commercial genetic testing services and therapeutics. The reality for many public healthcare providers is that it is difficult to obtain funding for single gene testing despite established correlations between genotype and therapeutic protocols; for example, the ketogenic diet in patients diagnosed with GLUT1 deficiency. A serious cost–benefit analysis of comprehensive genetic testing for epilepsy has not been conducted; however, it is likely that earlier genetic diagnosis would significantly reduce the economic burden of repeat hospitalisations associated with unnecessary investigations, and seizure exacerbation due to the inappropriate choice of antiepileptic drugs that may occur without an accurate diagnosis. We begin with a discussion of advances in understanding genetic epilepsies, beyond the classical Mendelian disorders, which are reviewed elsewhere, and then analyse recent clinical and research discoveries in epilepsy facilitated by MPS.
