
 epilepsy is a group of conditions characterized by recurrent , unprovoked seizures that result from abnormal synchronized neuronal firing in the brain .
epilepsy will affect up to 1 in 26 individuals and confers a significant health and economic burden .
there are many forms of epilepsy that can be distinguished by various characteristics including age of onset , predominant seizure type(s ) , and etiology .
three broad classes of epilepsy include genetic generalized epilepsy ( gge ; formerly idiopathic generalized epilepsy ) , focal epilepsy , and epileptic encephalopathy , though it should be noted that there are many specific epilepsy syndromes within each class ( table  1 ) . 
 table  1examples of epilepsy syndromesmajor classexamples of specific syndromesgenetic generalized epilepsy ( gge)juvenile myoclonic epilepsy ( jme)childhood absence epilepsy ( cae)generalized epilepsy with febrile seizures plus ( gefs+)focal epilepsytemporal lobe epilepsyautosomal dominant focal epilepsy with auditory features ( adpeaf)epileptic encephalopathyohtahara syndromedravet syndromewest syndrome examples of epilepsy syndromes the causes of epilepsy are diverse .
non - genetic or acquired etiologies account for 2030  % of cases and include stroke , head injury , and tumor . in the remaining cases , genetics
in fact , it has been recognized since the time of hippocrates that epilepsy is , at least in part , genetic .
modern evidence for genetic factors comes from twin studies , family studies , and the identification of single - gene disorders resulting in epilepsy syndromes .
studies in twins show an excess of disease concordance in monozygotic twins compared to dizygotic twins for most types of epilepsy . in a large australian cohort ,
generalized epilepsies showed the highest concordance ( ~80  % ) ; focal epilepsies have a lower ( 36  % ) but still significant concordance .
family studies reveal that the overall recurrence risk for epilepsy in first - degree relatives of affected individuals is 25  % [ 4 , 5 ] , and at least one study has shown that there is similar increased recurrence for family members of probands with either generalized or focal epilepsy .
finally , large multiplex families in which epilepsy segregates in an autosomal dominant manner have been used to identify linkage regions and causative genes in several different epilepsy syndromes . despite longstanding knowledge that epilepsy has a strong genetic component , it was not until 1995 that the first gene for a form of epilepsy was identified : mutations in the alpha 4 subunit of the nicotinic acetylcholine receptor , chrna4 , were identified in a large family with autosomal dominant nocturnal frontal lobe epilepsy ( adnfle ) .
since that time , multiple genes in which mutations cause epilepsy have been discovered [ 9 , 10 ] . while many epilepsy genes encode ion channel subunits , several non - channel genes encoding proteins important for brain development
copy number variants ( cnvs ) are large ( > 1  kb ) deletions or duplications of dna .
cnvs can contain zero , one , or many genes and have been increasingly recognized as an important source of both normal genetic variation and pathogenic mutation .
recurrent cnvs are deletions and duplications that occur as a result of non - allelic homologous recombination ( nahr ) at meiosis due to a predisposing sequence architecture : 50  kb to 10  mb of unique dna flanked by duplicated blocks of sequence that are > 10  kb with > 95  % sequence identity
. examples of recurrent cnvs associated with neurological or neurodevelopmental disorders include duplications of 17p12 causing charcot 
tooth type ia , deletions of 15q11-q13 in prader  willi and angelman syndromes [ 13 , 14 ] , and deletions of 7q11 causing williams 
beurens syndrome . because of the mechanism 
 by which they are generated , recurrent cnvs in two unrelated individuals with the same disorder have nearly identical breakpoints .
non - recurrent cnvs occur throughout the genome , but the breakpoints are not consistent .
while recurrent cnvs are generated by aberrant recombination , non - recurrent cnvs are often due to errors at replication .
there are several mechanisms for the generation of non - recurrent breakpoints that have been described , many of which involve microhomology  few to several identical base pairs at each breakpoint .
non - recurrent cnvs can be simple , where a stretch of dna is simply cut out of its original location and the ends rejoined , or complex , in which a deletion may be accompanied by insertion or duplication of dna at the breakpoints for example .
it is rare to find two or more patients with the same non - recurrent cnv .
however , comparison of overlapping cnvs in similarly affected patients often reveals a  smallest region of overlap  that can highlight one or a few genes as primarily responsible for the phenotype .
examples include the discovery of chd7 as the gene for charge syndrome , ehmt1 as the critical gene in 9q34 deletions ( kleefstra syndrome ) , and mbd5 in 2q23.1 deletions .
genome - wide identification of cnvs became efficient with the introduction of array comparative genomic hybridization ( cgh ) and single nucleotide polymorphism ( snp ) microarrays .
these technologies allow the detection of submicroscopic cnvs that are too small to be recognized by routine karyotype analysis . since the introduction of these technologies , the rate of discovery of submicroscopic rearrangements in both affected and unaffected individuals has increased dramatically .
the first large disease cohorts to be systematically studied were patients with intellectual disability ( i d ) , followed by autism and schizophrenia [ 28 , 29 ] .
comparison of cnvs in patients to those in controls combined with the identification of similar cnvs in multiple affected individuals led to the discovery of novel , disease - associated cnvs .
systematic cnv discovery in patients with epilepsy followed , and there has been steady progress that provides new insight into the genetics of epilepsy and related disorders . the remainder of this review will focus on cnv discovery and characterization in patients with epilepsy and recommendations for clinical testing .
the importance of non - recurrent cnvs in epilepsy has actually been known for some time .
for example , techniques such as quantitative pcr and multiplex ligation - dependent probe amplification ( mlpa ) have been used to detect single- and multiple - exon deletions and duplications in known genes such as scn1a [ 30 , 31 ] .
however , qpcr and mlpa are assays directed at specific locations in the genome , which means cnvs elsewhere will not be detected .
real advances in cnv discovery came from the application of genome - wide investigations using array cgh or snp microarrays .
heinzen and colleagues performed cnv discovery in a large cohort of 3812 patients with primarily focal epilepsy syndromes and identified an excess of large ( > 1  mb ) deletions in affected individuals , the majority of which were seen in one individual each [ 32 ] .
we performed array cgh studies in 517 patients with various types of epilepsy ( primarily generalized ) ;
~5  % of patients carried a non - recurrent cnv that affected at least one gene and was not seen in controls . in a study of 102 patients with epilepsy with or without other neurodevelopmental abnormalities , 23/102 individuals had at least one non - polymorphic cnv .
investigation of patients with epileptic encephalopathy syndromes also confirms the role of non - recurrent cnvs in severe epilepsies [ 35 ] .
together , these studies confirm that cnvs are important contributors to the genetics of broad classes of epilepsy .
because non - recurrent cnvs are rare and often unique , it can be difficult to interpret the clinical significance of any given cnv .
several criteria can be used , including size , gene content , presence or absence in control studies , and inheritance .
while a cnv in a single patient may be difficult to interpret , by collecting multiple patients with overlapping non - recurrent cnvs , it becomes possible to determine a critical region and , sometimes , a single critical gene for a given condition .
for example , depienne and colleagues   performed array cgh on a series of patient with a dravet - like syndrome and identified a single patient with a deletion involving pcdh19 on chromosome x. sequence analysis of the gene in additional patients revealed sequence mutations and established the gene as a cause of epilepsy restricted to females with i d . similarly , rare reports of deletions involving the grin2a gene highlighted the gene as a potentially important gene .
indeed , we and others have identified mutations in grin2a in 520  % of patients with epilepsy syndromes associated with language deficits ( epilepsy aphasia syndromes ) [ 39 , 40 , 41 ] .
we recently identified a patient with a large deletion of 15q26 ( reported in [ 42 ] ) . comparing the deletion in our patient to other 15q26 deletions in the literature
using high - throughput targeted sequencing of chd2 in 500 patients with epileptic encephalopathy , we identified de novo pathogenic mutations in 1.2  % of cases .
additional studies of overlapping rearrangements published in large disease cohorts , as well as smaller case reports , are likely to yield important causative genes .
a major  and somewhat surprising  advance in the field of epilepsy genetics has been the discovery of recurrent cnvs in patients .
the importance of recurrent cnvs as causes of i d syndromes , such as prader 
willi , angelman , smith  magenis , and velocardiofacial syndromes , has been known since the 1980s .
more recently , genome - wide cgh in large cohorts of patients with i d led to the identification of several novel recurrent microdeletion syndromes [ 29 , 44 ] .
the first study that highlighted the importance of cnvs in the genetic etiology of epilepsy was the discovery of recurrent 15q13.3 deletions in patients with generalized epilepsy [ 45 ] .
the 15q13.3 microdeletion ( chr15 : 31,000,00032,500,000 , hg19 ) was first described in patients with i d , but it was noted that most patients also suffered from seizures .
this observation led to a collaborative effort to determine the frequency of the deletion in a cohort of 1,223 patients with generalized epilepsy , most of whom did not have i d or other neurodevelopmental abnormalities . indeed
, 12/1,223 ( 1  % ) patients carried a 15q13.3 deletion compared to 0/3,699 control individuals [ 45 ] .
several subsequent studies confirmed this finding [ 33 , 47 , 48 ] , establishing the deletion as one of the most prevalent genetic risk factors for gge with an estimated odds ratio of 68 ( 29181 ) .
de kovel and colleagues investigated a cohort of 1,234 individuals with gge and 3,022 controls for recurrent cnvs .
in addition to 15q13.3 deletions , they found recurrent deletions at 16p13.11 ( chr16 : 15,500,00016,300,000 , hg19 ) and 15q11.2 ( chr15 : 22,800,00023,100,000 ,
hg19 ) in 0.5 and 1  % of patients , respectively , representing a significantly increased frequency compared to controls . heinzen and colleagues performed cnv genotyping in 3,812 individuals with epilepsy , most of which presented with a focal epilepsy syndrome [ 32 ] .
deletions of 16p13.11 were also enriched in patients compared to controls ( 23/3,812 vs 0/1299 ) . while 15q11.2 deletions were identified in 24/3,812 patients , there was not a significant enrichment compared to the frequency in controls ( 3/1,299 ) . in a study of 517 patients with various types of epilepsy , we identified five patients each with deletions at 15q11.2 , 15q11.3 , and 16p13.11 , again emphasizing the importance of each of these as frequent genetic susceptibility factors in epilepsy . of note , in an investigation of 315 patients with epileptic encephalopathy , there were no occurrences of 15q13.3 , 16p13.11 , or 15q11.2 deletions [ 35 ] , suggesting a different genetic architecture for this class of disorders .
each of the three epilepsy - associated recurrent deletions must be regarded as a risk factor for disease . in each case
, the deletion may be de novo or inherited from an affected or unaffected parent .
importantly , all three deletions also confer risk for other neurodevelopmental disorders . as described above , deletions of 15q13.3
were first identified in patients from an i d cohort . the deletion is also enriched in patients with schizophrenia [ 50 , 51 ] and is seen in patients with autism spectrum disorder and non - specific developmental delays [ 52 , 53 ] .
similarly , deletions of 16p13.11 and 15q11.2 are also associated with a wide range of neurodevelopmental and neuropsychiatric conditions [ 32 , 5457 ] .
interestingly , the 15q13.3 deletion appears to confer risk specifically for generalized forms of epilepsy  though present in 0.51  % of most gge cohorts , it was not reported in > 3,000 patients with focal epilepsy syndromes [ 32 ] . perhaps not surprisingly , patients with one of the epilepsy - associated recurrent deletions may present with a more severe phenotype than expected .
this is especially true for gge , which is not typically characterized by other neurocognitive deficits .
muhle and colleagues   identified 4/570 patients with various types of epilepsy who carried a 15q13.3 deletion .
detailed phenotype analysis revealed that all patients had absence epilepsy as well as some degree of i d .
more recently , a systematic comparison of the frequency of recurrent cnvs in patients with gge compared to patients with gge and i d showed that patients with  dual disability  are more likely to carry one of the three epilepsy - associated cnvs than patients with gge without other features [ 42 ] : 10  % of the gge  +  i d patients had one of the three recurrent cnvs compared to ~3  % of patients with gge but no i d .
other recurrent cnvs that are associated with neurodevelopmental disorders are also found in patients with epilepsy , though not as frequently as the three deletions discussed above [ 28 , 29 , 60 ] .
the role of cnvs in the genetic etiology of epilepsy has been clearly established , and diagnostic testing by chromosome microarray should be considered in this population .
there is a clear consensus that chromosome microarray testing should be the first - line test in the diagnosis of patients with neurodevelopmental disorders or multiple congenital anomalies .
given the overlapping genetic etiologies of a broad range of neurodevelopmental disorders , patients with epilepsy that is associated with other findings such as i d , autistic features , or developmental delays should be tested .
indeed , for gge with i d , the diagnostic yield will be 10  % or greater .
similarly , patients with brain malformations or other congenital abnormalities and patients with epileptic encephalopathy without a clear diagnosis should undergo cnv testing .
the yield of cnv testing in patients with epilepsy and no other features may be lower , but a cnv involving a known epilepsy gene would be an important diagnostic finding .
both recurrent and non - recurrent cnvs have been identified in most major classes of epilepsy . in some cases
, cnvs are highlighting the shared genetic susceptibility for a range of neurodevelopmental and neuropsychiatric conditions .
it is clear that the identification of disease - associated cnvs will lead to improved diagnosis and prognosis counseling .
recurrence risk counseling will remain complicated for cnvs with broad effects but is nevertheless an important consideration for families .
finally , as patients with shared genetic etiologies of epilepsy are identified , studies of genotype  phenotype correlation , natural history , and therapeutic response to specific anti - epileptic drugs can be performed , which will lead to improved long - term care and outcomes for patients .
 copy number variants ( cnvs ) are deletions or duplications of dna . 
 cnvs have been increasingly recognized as an important source of both normal genetic variation and pathogenic mutation . 
 technologies for genome - wide discovery of cnvs facilitate studies of large cohorts of patients and controls to identify cnvs that cause increased risk for disease . over the past 5  years 
 , studies of patients with epilepsy confirm that both recurrent and non - recurrent cnvs are an important source of mutation for patients with various forms of epilepsy . here 
 , we will review the latest findings and explore the clinical implications . 