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Utility of genetic testing in children with developmental and epileptic encephalopathy (DEE) at a tertiary hospital in South Africa: A prospective study
Abstract
Objectives
The developmental and epileptic encephalopathies (DEE) are a heterogeneous group of rare neurodevelopmental disorders, characterised by early-onset seizures that are often intractable, electroencephalographic abnormalities, and developmental delay or regression. There is a paucity of data from sub-Saharan Africa on the genetic basis of DEE. The aim of this study was to investigate the genetic background of DEE using targeted next generation sequencing (NGS) analysis in a tertiary pediatric neurology outpatient department at Tygerberg Hospital, South Africa. In addition, we assessed the value of the genetic results to the parents and managing physicians.
Methods
A prospective cohort study of 41 consecutive children with DEE (onset before 3 years of age) that were recruited over a 2-year period (2019-2021). Pre- and post-test genetic counselling were offered to all study participants. The results were categorized as either: positive (pathogenic/likely pathogenic variant identified), inconclusive (variant(s) of unknown significance identified), or negative (no variants identified). Result interpretation and careful matching of the variant to the clinical phenotype was performed. Subsequently, questionnaires were administered to both the physicians and the parents.
Results
A genetic underlying cause for DEE was identified in 18 of 41 children (diagnostic yield 43.9%). Variants in SCN1A (n=7), KANSL1 (n=2), KCNQ2 (n=2) and CDKL5 (n=2) were identified in more than one patient. Rarer genes included IQSEC2, SMC1A and STXBP1. All of the identified pathogenic variants fully explained and matched the respective phenotypic description of the patient at the time of clinical diagnosis. In 26% of patients the genetic result facilitated precision medicine management changes to anti-seizure medication. Both parents and physicians expressed benefit of genetic testing in patients with DEE.
Conclusion
Targeted NGS analysis proved an efficient diagnostic tool in detection of a genetic cause of DEE in a large proportion of South African children. The 43.9% diagnostic yield is similar to previously reported international pediatric cohorts. Additionally, the genetic findings proved useful for targeted therapeutic decision-making and accurate genetic counseling.
... An increasing number of single-gene disorders are being recognized as being associated with an IESS phenotype [10,12,13,[70][71][72][73][74][75]. Discussion of all attributable genes is beyond the scope of this review; we will focus on a sample of those which have been most commonly reported in the literature. ...
... Discussion of all attributable genes is beyond the scope of this review; we will focus on a sample of those which have been most commonly reported in the literature. Overall, some of the genes most frequently associated with IESS include pathogenic variants in TSC1, TSC2, CDKL5, ARX, KCNQ2, STXBP1, SCN2A and SCN8A, amongst others, although exact incidences of variants fluctuate between individual cohort studies [10,12,13,[70][71][72][73][74]. Moreover, genes associated with IESS have various patterns of inheritance, including de novo or autosomal dominant, autosomal recessive and X-linked patterns [10,12,13,[70][71][72][73][74]. ...
... Overall, some of the genes most frequently associated with IESS include pathogenic variants in TSC1, TSC2, CDKL5, ARX, KCNQ2, STXBP1, SCN2A and SCN8A, amongst others, although exact incidences of variants fluctuate between individual cohort studies [10,12,13,[70][71][72][73][74]. Moreover, genes associated with IESS have various patterns of inheritance, including de novo or autosomal dominant, autosomal recessive and X-linked patterns [10,12,13,[70][71][72][73][74]. ...
Infantile epileptic spasms syndrome (IESS) is a devastating developmental epileptic encephalopathy (DEE) consisting of epileptic spasms, as well as one or both of developmental regression or stagnation and hypsarrhythmia on EEG. A myriad of aetiologies are associated with the development of IESS; broadly, 60% of cases are thought to be structural, metabolic or infectious in nature, with the remainder genetic or of unknown cause. Epilepsy genetics is a growing field, and over 28 copy number variants and 70 single gene pathogenic variants related to IESS have been discovered to date. While not exhaustive, some of the most commonly reported genetic aetiologies include trisomy 21 and pathogenic variants in genes such as TSC1, TSC2, CDKL5, ARX, KCNQ2, STXBP1 and SCN2A. Understanding the genetic mechanisms of IESS may provide the opportunity to better discern IESS pathophysiology and improve treatments for this condition. This narrative review presents an overview of our current understanding of IESS genetics, with an emphasis on animal models of IESS pathogenesis, the spectrum of genetic aetiologies of IESS (i.e., chromosomal disorders, single-gene disorders, trinucleotide repeat disorders and mitochondrial disorders), as well as available genetic testing methods and their respective diagnostic yields. Future opportunities as they relate to precision medicine and epilepsy genetics in the treatment of IESS are also explored.
... A third published record with 100% yield was a study of 41 children with suspected DEE who underwent genomic investigations, two of whom had reported symptoms of developmental regression. Both children received an explanatory genomic result (Essajee et al., 2022). Sensitivity and meta-analysis analysis was completed for all studies (see supplementary material Table iii) and for subgroups (see supplementary material Table iv). ...
... When childhood conditions were grouped, children with developmental regression and neurological signs (Ma et al., 2013;Muthaffar, 2021), or with suspected DEE (Essajee et al., 2022;Hong et al., 2020), or suspected Rett syndrome (Iwama et al., 2019) were more likely to receive a diagnostic result than children investigated for an inborn error of metabolism (Romao et al., 2017), or autistic children with developmental regression (Byrne et al., 2023;Kosinovsky et al., 2005;Parmeggiani et al., 2010). There was an overall 40% diagnostic yield for children with developmental regression and developmental delay, higher than for children with suspected inborn errors or metabolism (10%) and autistic children (9%). ...
This systematic review evaluates the diagnostic yield of investigations requested for children with developmental regression. Online databases MEDLINE, EMBASE, CINAHL, PsycINFO, Cochrane were searched to identify published records that reported a diagnostic yield for children with developmental regression. Random effects meta-analyses were performed using R software with meta package. Our search identified 11,283 published records, of which 347 were assessed for eligibility, and 15 (596 children) were included in the final systematic review and meta-analysis. Subgroup analysis assessed the diagnostic yield for investigating children with different presentations and developmental regression. Diagnostic yield results were 68% for children with neurological symptoms (two records, six children, 95%CI 32–100) and children with epileptic symptoms (two records, 56 children, 95%CI 15–100); 40% for children with neurodevelopmental delay (six records, 294 children, 95%CI 3–78); 9% for autistic children (three records, 138 children, 95%CI 0–26). Pooled analysis could not be completed for metabolic (one record, 29 children) or genetic presentations (one record, 73 children). The diagnostic yield for genetic/genomic investigations (six records, 142 children, 95%CI, 47–92) was 70%, compared with 28% for metabolic (five records, 286 children, 95%CI 0–64), 13% for neurophysiological (two records, 127 children, 95%CI 0–39) and 6% for neuroimaging (two records, 41 children, 95%CI 0–20). Investigations for children with developmental regression and neurological or epileptic symptoms resulted in the highest diagnostic yield. These results are clinically meaningful and will inform future research to advance towards an agreed investigative approach yet lack statistical significance due to small samples.
... 14 The relevance of early diagnosis of monogenic epilepsies is undeniable and avoids the lengthy diagnostic odyssey. [15][16][17][18][19] It also allows families to connect with support groups or organizations and seek information or inclusion in clinical trials. 20 Regarding treatment, epilepsy management is challenging since pharmacological and non-pharmacological treatments have limited value in seizure control. ...
... Socioeconomic factors play a major role in genetic conditions worldwide. 15 It is well-documented that patients with lower income and underserved minorities experience significant delays in genetic testing. [37][38][39] Delays in referral and lengthy waiting for tertiary care centers are identified as key factors postponing the diagnosis in public and private settings. ...
Objectives
This study aims to determine the current state of CDD diagnosis and epilepsy treatment in an upper‐middle‐income country.
Methods
Forty‐seven families of the Brazilian CDD Association were invited to participate in an online survey to gather information about the diagnosis and treatment of epilepsy.
Results
Forty‐three families (91.5%) of unrelated patients with confirmed genetic diagnosis of CDD participated. The median age was 7 years (ranging from 1.3–25 years) and the male: female ratio was 1:6. Early and severe epilepsy started during infancy in 74.4%. Seizures occurred daily in 61.9% and 83.7% had clusters of seizures. The mean age of diagnosis was 3.3 years (ranging from 37 days to 16 years), and younger patients had an earlier diagnosis (p < 0.001). Patients were seen by an average of 4.4 physicians (1–15) before the diagnosis. The most relevant obstacles to genetic testing were cost (55.8%) and late requests by physicians (27.9%). At the moment of the assessment, patients received a mean of 3.6 ASMs/day (ranging from 1 to 5). Thirty‐four (79.1%) caregivers reported side effects throughout life, including life‐threatening events in 16.3%.
Significance
Based on our findings, a sense of urgency for genetic assessment implementation is evident since the delay in the diagnosis with unnecessary use of resources and excessive polytherapy with serious side effects cause a higher burden to the healthcare system, caregivers, and patients.
Plain Language Summary
In this study, we assessed the diagnosis and treatment of patients with genetically confirmed DEE‐CDKL5 from the Brazilian Association of CDD with an online survey. Caregivers reported a long delay in the diagnosis associated with cost and late referral to genetic testing, considered the last resource for one‐third of the patients. Patients received a high number of ASM, mainly under polytherapy, with serious side effects. Although it is promising that younger patients received earlier diagnosis, public policies for genetic testing are needed to improve CDD patients' care.
... 3,19 There was a slight female preponderance in our study which is in line with other studies. 9,20 In our study, the yield between WES, FES, and EGP did not reach statistical significance (p = .07). Yield was maximum with WES and FES, identifying P/LP variants in 16/24 (66.7%) and 14/21 (66.7%) cases respectively. ...
... 25 Yield was higher in an African study (43.9%) exclusively on DEE. 20 It was also higher (48%) in a study with a mixed cohort of epilepsies and EE. 26 Our higher yield compared with other studies could be due to the well characterization of the epilepsy syndromes. Specific diagnoses for traditional genes involved in DEEs were established in our study, including seven cases of SCN1A-positive DS where clinical suspicion was high. ...
Objective
Studies on the genetic yield of developmental and epileptic encephalopathy and Epileptic encephalopathies using next‐generation sequencing techniques are sparse from the Indian subcontinent. Hence, the study was conducted to assess the yield of genetic testing and the proportion of children where a positive genetic yield influenced treatment decisions.
Methods
In this retrospective observational study, electronic medical records of children (0–12 years) with suspected genetic epilepsy who underwent genetic testing using whole exome sequencing, focused exome sequencing and epilepsy gene panels were retrieved. Genetic yield was ascertained based on the detection of pathogenic and likely pathogenic variants.
Results
A total of 100 patients with epilepsy underwent genetic testing. A yield of 53.8% (42/78) was obtained. Pathogenic variants were identified in 18 (42.8%) cases and likely pathogenic variants in 24 (57.1%) cases. Yield was 66.6% each through whole exome sequencing, focused exome sequencing and 40% through Epilepsy gene panels (p = .07). Yield was not statistically significant across different age groups (p = .2). It was however found to significantly vary across different epilepsy syndromes with maximum yield in Epilepsy in infancy with migrating focal seizures in 2 (100%), followed by developmental and epileptic encephalopathy unspecified in 14 (77.7%), Dravet syndrome in 14 (60.8%), early infantile developmental and epileptic encephalopathy in 3 (60%), infantile epileptic spasm syndrome in 5 (35.7%), and other epileptic encephalopathies in 4 (30.7%) cases (p = .04). After genetic diagnosis and drug optimization, drug‐refractory proportion reduced from 73.8% to 45.3%. About half of the cases achieved seizure control.
Significance
A reasonably high yield of 53.8% was obtained irrespective of the choice of panel or exome or age group using next‐generation sequencing‐based techniques. Yield was however higher in certain epilepsy syndromes and low in Infantile epileptic spasms syndrome. A specific genetic diagnosis facilitated tailored treatment leading to seizure freedom in 28.6% and marked seizure reduction in 54.7% cases.
... Gene-phenotype matching Supplementary Table 5 shows details of the patients in whom a diagnosis could be made definitively, along with the pathogenic variants identified. 17 children with developmental epileptic encephalopathies (DDE) from a previous study were included in Supplementary Table 5, as they were all tested within the same time frame [4]. A total of 46% (26/56) of patients had an autosomal dominant, 30% an autosomal recessive (17/56 -10/17 homozygous and 7/17 compound heterozygous) and 23% (13/56) an X-linked condition. ...
... In almost half of the cases, treatment was adjusted to some extent once the pathogenic variant was known. Treatment changes included adjusting anti-seizure medications e.g., stopping sodium channel blockers like Lamotrigine in patients with SCN1A or adding sodium channel blockers like carbamazepine in patients with KCNQ2 pathogenic variants [4]. The questionnaire was given to parents only and not the treating physicians therefore full details of treatment changes were not covered by this study. ...
Next generation sequencing (NGS)-based tests have become routine first-line investigative modalities in paediatric neurology clinics in many high-income countries (HICs). Studies from these countries show that these tests are both cost-effective and reliable in diagnosing many complex childhood neurological diseases. However, NGS-based testing in low-and middle-income countries (LMICs) is limited due to affordability constraints. The primary objective of this study was to evaluate the diagnostic yield and impact of targeted gene panel sequencing in a selected paediatric cohort attending a tertiary paediatric neurology clinic in the Western Cape Province of South Africa. This retrospective study included 124 consecutive paediatric patients with neurological disease, aged 6 weeks to 17 years, referred for NGS-based multi-gene panel testing over a 41-month period. Twenty-four different disease group-specific panels were utilized. A caregiver experience questionnaire was administered when a pathogenic variant was identified. The overall study diagnostic yield (DY) was 45% (56/124 patients). The diagnostic yield in this study is similar to previously reported paediatric cohorts in HICs. The high yields for neuromuscular disorders (52%) and early epileptic encephalopathies (41%) suggest that NGS-based panels may be more cost-effective as first-line testing in well-defined phenotypes. The latter finding argues for early inclusion of all children with developmental epileptic encephalopathies (DEE), as early diagnosis leads to better treatment and avoidance of unnecessary investigations.
... It was concerned with the development of a DEE panel in the South African region. 6 Therefore, exploration of the etiology of DEE and the early diagnosis of causal variants by next-generation sequencing (NGS) assist to a great extent in terms of alleviating social and economic problems. Scrutinizing through literature, multiple research works tackled the use of gene panels in epilepsy with variable diagnostic yields. ...
... In Africa, only one study has recently been published which was concerned with the South African population. 6 However, in North Africa (Tunisia, Egypt, Libya, Algeria, Morocco), no study on this issue has been undertaken before. In the Arabic countries, only one study was published in the Saudi Arabia region using WES/ WGS sequencing rather than panels. ...
Objective
To develop a high‐throughput sequencing panel for the diagnosis of developmental and epileptic encephalopathy in Tunisia and to clarify the frequency of disease‐causing genes in this region.
Methods
We developed a custom panel for next‐generation sequencing of the coding sequences of 116 genes in individuals with developmental and epileptic encephalopathy from the Tunisian population. Segregation analyses and in silico studies have been conducted to assess the identified variants' pathogenicity.
Results
We report 12 pathogenic variants in SCN1A, CHD2, CDKL5, SZT2, KCNT1, GNAO1, PCDH19, MECP2, GRIN2A, and SYNGAP1 in patients with developmental and epileptic encephalopathy. Five of these variants are novel: “c.149delA, p.(Asn50MetfsTer26)” in CDKL5; “c.3616C > T, p.(Arg1206Ter)” in SZT2; “c.111_113del, p.(Leu39del)” in GNAO1; “c.1435G>C, p.(Asp479His)” in PCDH19; and “c.2143delC, p.(Arg716GlyfsTer10)” in SYNGAP1. Additionally, for four of our patients, the genetic result facilitated the choice of the appropriate treatment.
Significance
This is the first report of a custom gene panel to identify genetic variants implicated in developmental and epileptic encephalopathy in the Tunisian population as well as the North African region (Tunisia, Egypt, Libya, Algeria, Morocco) with a diagnostic rate of 30%. This high‐throughput sequencing panel has considerably improved the rate of positive diagnosis of developmental and epileptic encephalopathy in the Tunisian population, which was less than 15% using Sanger sequencing. The benefit of genetic testing in these patients was approved by both physicians and parents.
... GABA A -receptor subunits can mix and match to form a wealth of receptor subtypes. While this could theoretically give a staggering number of potential receptor combinations, only a limited number (Enna & McCarson, 2006;Enz, 2001;Essajee et al., 2022;Eugène et al., 2007;Fedi et al., 2006;Ferguson & Cardin, 2020;Fisher, 2004;Fisher et al., 2014;Frugier et al., 2007;Fu et al., 2022;Gielen et al., 2012) of subtypes are believed to be naturally expressed in the mammalian brain (Mortensen et al., 2011;Olsen & Sieghart, 2009;Richard & Werner, 2008;Whiting, 2003). The most common isoforms are composed of two α's, two β's and either a γ2 or δ subunit, and of these three receptor subtypes, α1β2/3γ2, α2β2/3γ2 and α3β2/3γ2, are believed to constitute the vast majority (~80%) of receptors in the brain. ...
... DEE is characterised by young age of seizure onset, pharmacoresistant epilepsy, developmental delay, and abnormal electroencephalographic findings Mierzewska et al., 2021). Clinical manifestations of DEE are on a spectrum but may include varying degrees of neurodevelopmental impairment such as developmental delay and intellectual disability varying from mild to severe, microcephaly, movement disorders, hypotonia, autism spectrum disorders and behavioural difficulties (Essajee et al., 2022;Kang et al., 2021;Matricardi et al., 2020;. Specific electroclinical syndromes classified as DEE include Dravet syndrome, Ohtahara syndrome, Lennox-Gastaut syndrome (LGS), West syndrome and epilepsy of infancy with migrating focal seizures. ...
Normal brain function requires a tightly regulated balance between excitatory and inhibitory neurotransmissions. γ‐Aminobutyric acid type A (GABAA) receptors represent the major class of inhibitory ion channels in the mammalian brain. Dysregulation of these receptors and/or their associated pathways is strongly implicated in the pathophysiology of epilepsy. To date, hundreds of different GABAA receptor subunit variants have been associated with epilepsy, making them a prominent cause of genetically linked epilepsy. While identifying these genetic variants is crucial for accurate diagnosis and effective genetic counselling, it does not necessarily lead to improved personalised treatment options. This is because the identification of a variant does not reveal how the function of GABAA receptors is affected. Genetic variants in GABAA receptor subunits can cause complex changes to receptor properties resulting in various degrees of gain‐of‐function, loss‐of‐function or a combination of both. Understanding how variants affect the function of GABAA receptors therefore represents an important first step in the ongoing development of precision therapies. Furthermore, it is important to ensure that functional data are produced using methodologies that allow genetic variants to be classified using clinical guidelines such as those developed by the American College of Medical Genetics and Genomics. This article will review the current knowledge in the field and provide recommendations for future functional analysis of genetic GABAA receptor variants. image
... GABA A -receptor subunits can mix and match to form a wealth of receptor subtypes. While this could theoretically give a staggering number of potential receptor combinations, only a limited number (Enna & McCarson, 2006;Enz, 2001;Essajee et al., 2022;Eugène et al., 2007;Fedi et al., 2006;Ferguson & Cardin, 2020;Fisher, 2004;Fisher et al., 2014;Frugier et al., 2007;Fu et al., 2022;Gielen et al., 2012) of subtypes are believed to be naturally expressed in the mammalian brain (Mortensen et al., 2011;Olsen & Sieghart, 2009;Richard & Werner, 2008;Whiting, 2003). The most common isoforms are composed of two α's, two β's and either a γ2 or δ subunit, and of these three receptor subtypes, α1β2/3γ2, α2β2/3γ2 and α3β2/3γ2, are believed to constitute the vast majority (~80%) of receptors in the brain. ...
... DEE is characterised by young age of seizure onset, pharmacoresistant epilepsy, developmental delay, and abnormal electroencephalographic findings Mierzewska et al., 2021). Clinical manifestations of DEE are on a spectrum but may include varying degrees of neurodevelopmental impairment such as developmental delay and intellectual disability varying from mild to severe, microcephaly, movement disorders, hypotonia, autism spectrum disorders and behavioural difficulties (Essajee et al., 2022;Kang et al., 2021;Matricardi et al., 2020;Strzelczyk & Schubert-Bast, 2022). Specific electroclinical syndromes classified as DEE include Dravet syndrome, Ohtahara syndrome, Lennox-Gastaut syndrome (LGS), West syndrome and epilepsy of infancy with migrating focal seizures. ...
Objective:
Variants in GABRA1 have been associated with a broad epilepsy spectrum, ranging from genetic generalized epilepsies to developmental and epileptic encephalopathies. However, our understanding of what determines the phenotype severity and best treatment options remains inadequate. We therefore aimed to analyse the electro-clinical features and the functional effects of GABRA1-variants to establish genotype-phenotype correlations.
Methods:
Genetic and electro-clinical data of 27 individuals (22 unrelated and 2 families) harbouring 20 different GABRA1 variants were collected and accompanied with functional analysis of 19 variants.
Results:
Individuals in this cohort could be assigned into different clinical subgroups based on the functional effect of their variant and its structural position within the GABRA1 subunit. A homogenous phenotype with mild cognitive impairment and infantile-onset epilepsy (focal seizures, fever sensitivity and EEG posterior epileptiform discharges) was described for variants in the extra-cellular domain and the small transmembrane loops. These variants displayed loss-of-function (LoF) effects and the patients generally had a favourable outcome. A more severe phenotype was associated with variants in the pore-forming transmembrane helices. These variants displayed either gain-of-function (GoF) or LoF effects. GoF-variants were associated with severe early-onset neurodevelopmental disorders, including early infantile developmental and epileptic encephalopathy.
Interpretation:
Our data expand the genetic and phenotypic spectrum of GABRA1-epilepsies and permit to delineate specific sub-phenotypes for LoF and GoF variants, though the heterogeneity of phenotypes and variants. Generally, variants in the transmembrane helices cause more severe phenotypes, in particular GoF variants. These findings establish the basis for a better understanding of the patho-mechanism and precision medicine approach in GABRA1-related disorders. Further studies in larger populations are needed to provide a conclusive genotype-phenotype correlation. This article is protected by copyright. All rights reserved.
... However, only studies from the last 10 years demonstrate the integration of Next Generation Sequencing (NGS) and the exploration of point-of-care genetic testing models to illustrate the technological advancements influencing genetic practices in the region. 38,39 At the same time, ethical challenges, such as the return of incidental findings and navigating the complexities of genetics for conditions like schizophrenia are explored, highlighting the need for ethical guidelines and considerations in genetic research and counseling. 40 The results in the column with the outcomes span a wide range of information, from the effectiveness of counseling and patient understanding to decisionmaking regarding prenatal screening and managing hereditary diseases to evaluating genetic testing technologies and exploring the emotional and ethical aspects of genetic counseling. ...
... Since then, two prospective studies employing molecular testing on a cohort of patients with developmental and epileptic encephalopathies (DEE) have been performed in South Africa. Essajee et al. revealed a noteworthy diagnostic yield of next-generation sequencing (NGS) analysis, identifying pathogenic variants in 18/41 (43.9%) patients by a panel of 308 genes [56]. Esterhuizen et al. analyzed a cohort of children with DEE by means not only of a gene panel built on 71 DEE-associated genes, but also by chromosomal microarray and exome sequencing. ...
Background/Objectives: Epilepsy is a major public health issue in Sub-Saharan Africa, particularly among children, due to limited healthcare resources, socioeconomic inequalities, and cultural stigma that often result in underdiagnosis and undertreatment. This review examines pediatric epilepsy’s diagnosis, classification, and management in this setting, highlighting the need for culturally appropriate interventions to improve care quality and address these challenges. Methods: A review of the literature was conducted using MEDLINE, Embase, Scopus, and Web of Science databases to identify pertinent studies published between 2013 and 2024. This review included studies examining the epidemiology, seizure classification and etiologies of epilepsy among children in Sub-Saharan Africa. Results: This review revealed higher incidence and prevalence of epilepsy in Sub-Saharan Africa compared to high-income countries, primarily attributable to factors such as infectious diseases, perinatal injuries, and limited diagnostic resources. The most frequently reported types of epilepsy were generalized and focal seizures, with significant etiological contributions from structural and infectious causes, including nodding syndrome and HIV-related epilepsy. The treatment gap remains considerable, with up to 80% of children not receiving appropriate antiseizure medications. Conclusions: The diagnosis and treatment of epilepsy in pediatric populations in Sub-Saharan Africa is complicated by several factors, including cultural stigma and the lack of adequate healthcare infrastructure. There is an urgent need for culturally tailored diagnostic tools, improved access to affordable treatments, and public health initiatives aimed at reducing stigma. Addressing these gaps through enhanced research, improved healthcare access, and targeted educational campaigns is crucial for improving the quality of life for children with epilepsy.
... Due to the pleiotropic nature of STXBP1, it has become one of the most identified variants of concern, with a recent study of 150 children with EIEE identifying STXBP1 variants in 6% of infantile onset epilepsy patients, and 10% of neonatal onset epileptic encephalopathy [3]. It has often been identified as one of the top five causative genes in a variety of genetic screening studies including infantile spasms [4][5][6][7], DEE [8][9][10], EIEE [11], and a combination of ID, GDD, and autism spectrum disorder [12]. Due to its importance within the cell and its role in clinical disease, STXBP1 has become an area of research interest. ...
In recent years, the affordability and availability of genetic testing have led to its increased use in clinical care. The increased frequency of testing has led to STXBP1 variants being identified as one of the more common variants associated with neurological disorders. In this review, we aim to summarize the common clinical phenotypes associated with STXBP1 pathogenic variants, provide an overview of their known natural history, and discuss current research into the genotype to phenotype correlation. We will also provide an overview of the suspected normal function of the STXBP1-encoded Munc18-1 protein, animal models, and experimental techniques that have been developed to study its function and use this information to try to explain the diverse phenotypes associated with STXBP1-related disorders. Finally, we will explore current therapies for STXBP1 disorders, including an overview of treatment goals for STXBP1-related disorders, a discussion of the current evidence for therapies, and future directions of personalized medications for STXBP1-related disorders.
... The genetic factors behind EIEE were initially discovered in 2001 and are mainly associated with single-gene variants, although abnormal chromosomal structures and polygenic regulation can also be causative factors. The genetics of EIEE were identified in approximately 40% of cases (Claes et al., 2001;Essajee et al., 2022;Liu et al., 2021), and since the degree of phenotypic and genetic heterogeneity in EIEE is high, the relationship between clinical phenotypes and genotypes cannot be generalized. Single-gene variants can cause different clinical phenotypes, whereas different variants of various genes can equally lead to similar clinical phenotypes. ...
Background:
Early infantile epileptic encephalopathy (EIEE) is a group of highly heterogeneous diseases, both phenotypically and genetically. Usually, it starts early on and manifests as intractable epilepsy, abnormal electroencephalogram, and growth retardation/intellectual impairment. With the advent of next-generation sequencing (NGS), its genetic etiology has attracted increasing clinical attention. This study aimed to investigate the genetic characteristics and clinical phenotypes of patients with EIEE from a central hospital in Eastern China.
Methods:
This study retrospectively included the gene variants from 24 EIEE-positive patients admitted between January 2021 and January 2022 to a hospital in Anhui Province, China. The genetic diagnosis was performed in all cases by trio-based whole-exome sequencing (WES). Additionally, Video electroencephalogram (VEEG) and neuroimaging examinations were performed.
Results:
A total of 24 children were included. The average age at the first seizure was approximately 5 months. About 42% of children had developmental retardation of varying degrees, 43% had brain structural abnormalities, and 64% had VEEG abnormalities. In addition, other phenotypes, including endocrine metabolism and cardiac structural abnormalities, have been independently reported. In total, fifteen pathogenic gene variants were identified in 24 patients. The main pathogenic genes identified were SCN1A (25%, 6/24), KCNQ2 (8.3%, 2/24), and TBC1D24 (8.3%, 2/24). We also found an extremely rare case of EIEE84 type caused by biallelic UGDH gene variants, predicting that this variant might affect the stability of the protein structure.
Conclusions:
SCN1A pathogenic variants are the main factor leading to EIEE, similar to previously published cohort reports. NGS is useful for accurate clinical diagnoses and precise treatment choices. We also reported a rare case of EIEE84 caused by variants in the UGDH gene in a Chinese patient. This study further enriches the known spectrum of pathogenic EIEE genes.
... Gene-phenotype matching Table 3 shows the gene-phenotype correlation of the study population. Children with developmental epileptic encephalopathies (DDE) were excluded as they were described in a previous publication from our institution (4). For recessively inherited conditions, we noted the following: the diagnosis was con rmed in four patients (patients 62, 67, 79 and 92) as they were compound heterozygous for pathogenic variants in RYR1, RYR1, PCCA and ARSA, respectively. ...
Next generation sequencing (NGS)-based tests have become routine first-line investigative modalities in paediatric neurology clinics in many high-income countries (HICs). Studies from these countries show that these tests are both cost-effective and reliable in diagnosing many complex childhood neurological diseases; however, NGS-based testing in low-and middle-income countries (LMICs) is limited due to cost. The primary objective of this study was to evaluate the diagnostic yield and impact of targeted gene panels in a selected paediatric cohort attending a tertiary paediatric neurology clinic in the Western Cape Province of South Africa. This retrospective study included 124 consecutive paediatric patients with neurological disease, referred for multi-gene panel testing over a 41-month period. Twenty-four different disease group-specific panels were utilized. A caregiver experience questionnaire was administered when a pathogenic variant was identified. The overall study diagnostic yield (DY) was 53% (66/124 patients). It was highest for neuromuscular disorders 64% (16/25), cerebral palsy spectrum disorders 54% (9/16) and early-onset epilepsies 44% (28/63). Testing proved inconclusive (variants of uncertain significance) in 38% (47/124). The majority of caregivers (97%) viewed NGS-based testing as a positive experience.
The diagnostic yield in this study is similar to previously reported paediatric cohorts in HICs. The high yields for neuromuscular disorders and early epileptic encephalopathies suggest that NGS-based panels may be more cost-effective as first-line testing in well-defined phenotypes. The latter finding argues for early inclusion of all children with developmental epileptic encephalopathies (DEE), as early diagnosis leads to better treatment and avoidance of unnecessary investigations.
... Certain genetic mutations can provide therapeutic options that may be more effective for a particular patient. Based on current clinical evidence, some precision medicine strategies for epilepsy have been proposed [66,67]. However, early genetic testing is only the first step in the precise approach; functional testing is also required to determine pathogenicity and explore the fundamental functional impact, such as in the case of the SCN1A variant [68][69][70]. ...
Advances in disease-related gene discovery have led to tremendous innovations in the field of epilepsy genetics. Identification of genetic mutations that cause epileptic encephalopathies has opened new avenues for the development of targeted therapies. Clinical testing using extensive gene panels, exomes, and genomes is currently accessible and has resulted in higher rates of diagnosis and better comprehension of the disease mechanisms underlying the condition. Children with developmental disabilities have a higher risk of developing epilepsy. As our understanding of the mechanisms underlying encephalopathies and epilepsies improves, there may be greater potential to develop innovative therapies tailored to an individual’s genotype. This article provides an overview of the significant progress in epilepsy genomics in recent years, with a focus on developmental and epileptic encephalopathies in children. The aim of this review is to enhance comprehension of the clinical utilization of genetic testing in this particular patient population. The development of effective and precise therapeutic strategies for epileptic encephalopathies may be facilitated by a comprehensive understanding of their molecular pathogenesis.
Background Developmental and Epileptic Encephalopathies stand for a heterogenous group of epileptic syndromes, where the epileptic activity itself and/or the etiology contribute to cognitive and behavioral impairment. In recent decades, genetic etiology has increasingly been recognized as the cause of Developmental and Epileptic Encephalopathies and numerous genes have been identified, thanks to advances in genetic technologies. These discoveries have enabled precision treatments for several syndromes. Therefore, the identification of the causal variant in a gene is an intrinsic starting point to specify a precision therapy for the patient and an adequate management.
Results We developed a custom panel for Next Generation Sequencing of the coding sequences of 116 genes in individuals with Developmental and Epileptic Encephalopathy from the Tunisian population. Segregation analyses as well as in silico studies have been conducted to assess the identified variants’ pathogenicity. We report 12 pathogenic variants in SCN1A, CHD2, CDKL5, SZT2, KCNT1, GNAO1, PCDH19, MECP2, GRIN2A, and SYNGAP1 in patients with Developmental and Epileptic Encephalopathy. Five of these variants are novel: “c.149delA, p.(Asn50MetfsTer26)” in CDKL5; “c.3616C>T, p.(Arg1206Ter)” in SZT2; “c.111_113del, p.(Leu39del)” in GNAO1; “c.1435G>C , p.(Asp479His)” in PCDH19; as well as “c.2143delC, p. (Arg716GlyfsTer10)”in SYNGAP1. Additionally, for five of our patients, the genetic result facilitated the choice of the appropriate treatment.
Conclusion This is the first report of a custom gene panel to identify genetic variants implicated in Developmental and Epileptic Encephalopathy in the Tunisian population as well as the North African region (Tunisia, Egypt, Libya, Algeria, Morocco) with a diagnostic rate of 30%. This high-throughput sequencing panel has considerably improved the rate of positive diagnosis of Developmental and Epileptic Encephalopathy in the Tunisian population, which was less than 15% using Sanger sequencing. The benefit of genetic testing in these patients was approved by both physicians and parents.
Genetic sequencing technologies have led to an increase in the identification and characterization of monogenic epilepsy syndromes. This increase has, in turn, generated strong interest in developing “precision therapies” based on the unique molecular genetics of a given monogenic epilepsy syndrome. These therapies include diets, vitamins, cell-signaling regulators, ion channel modulators, repurposed medications, molecular chaperones, and gene therapies. In this review, we evaluate these therapies from the perspective of their clinical validity and discuss the future of these therapies for individual syndromes.
Genomic testing is becoming routine for diagnosing rare childhood genetic disease. Evidence underlying sustainable implementation is limited, focusing on short-term endpoints such as diagnostic yield, unable to fully characterize patient and family valued outcomes. Although genomic testing is becoming widely available, evidentiary and outcomes uncertainty persist as key challenges for implementation. We examine whether the current evidence base reflects public tolerance for uncertainty for genomics to diagnose rare childhood genetic disease. We conducted focus groups with general population parents in Vancouver, Canada, and Oxford, United Kingdom, to discuss expectations and concerns related to genomic testing to diagnose rare childhood genetic disease. Applying a purposive sampling technique, recruitment continued until thematic saturation was reached. Transcripts were analysed using thematic analysis. Thirty-three parents participated across four focus groups. Participants valued causal diagnoses alongside management strategies to improve patient health and wellbeing. Further, participants valued expanding the evidence base to reduce evidentiary uncertainty while ensuring security of information. Willingness to pay out of pocket for testing reflected perceived familial health benefit. Diagnostic yield fails to fully capture valued outcomes, and efforts to resolve uncertainty better reflect public priorities. Evaluations of genomic testing that fully integrate valued endpoints are necessary to ensure consistency with best practices and public willingness to accept the uncertain familial benefit.
The term “developmental and epileptic encephalopathy” (DEE) refers to when cognitive functions are influenced by both seizure and interictal epileptiform activity and the neurobiological process behind the epilepsy. Many DEEs are related to gene variants and the onset is typically during early childhood. In this setting, neurocognition, whilst not improved by seizure control, may benefit from some precision therapies. In patients with non‐progressive diseases with cognitive impairment and co‐existing epilepsy, in whom the epileptiform activity does not affect or has minimal effect on function, the term “developmental encephalopathy” (DE) can be used. In contrast, for those patients with direct impact on cognition due to epileptic or epileptiform activity, the term “epileptic encephalopathy” (EE) is preferred, as most can revert to their normal or near normal baseline cognitive state with appropriate intervention. These children need aggressive treatment. Clinicians must tailor care towards individual needs and realistic expectations for each affected person; those with DE are unlikely to gain from aggressive antiseizure medication whilst those with EE will gain. Patients with DEE might benefit from a precision medicine approach in order to reduce the overall burden of epilepsy.
Objective
Early identification of de novo KCNQ2 variants in patients with epilepsy raises prognostic issues toward optimal management. We analyzed the clinical and genetic information from a cohort of patients with de novo KCNQ2 pathogenic variants to dissect genotype-phenotype correlations.
Methods
Patients with de novo KCNQ2 pathogenic variants were identified from Italy, Denmark, and Belgium. Atomic resolution Kv7.2 structures were also generated using homology modeling to map the variants.
Results
We included 34 patients with a mean age of 4.7 years. Median seizure onset was 2 days, mainly with focal seizures with autonomic signs. Twenty-two patients (65%) were seizure free at the mean age of 1.2 years. More than half of the patients (17/32) displayed severe/profound intellectual disability; however, 4 (13%) of them had a normal cognitive outcome.
A total of 28 de novo pathogenic variants were identified, most missense (25/28), and clustered in conserved regions of the protein; 6 variants recurred, and 7 were novel. We did not identify a relationship between variant position and seizure offset or cognitive outcome in patients harboring missense variants. Besides, recurrent variants were associated with overlapping epilepsy features but also variable evolution regarding the intellectual outcome.
Conclusions
We highlight the complexity of variant interpretation to assess the impact of a class of de novo KCNQ2 mutations. Genetic modifiers could be implicated, but the study paradigms to successfully address the impact of each single mutation need to be developed.
Glut1 deficiency syndrome (Glut1DS) is a brain energy failure syndrome caused by impaired glucose transport across brain tissue barriers. Glucose diffusion across tissue barriers is facilitated by a family of proteins including glucose transporter type 1 (Glut1). Patients are treated effectively with ketogenic diet therapies (KDT) that provide a supplemental fuel, namely ketone bodies, for brain energy metabolism. The increasing complexity of Glut1DS, since its original description in 1991, now demands an international consensus statement regarding diagnosis and treatment. International experts (n = 23) developed a consensus statement utilizing their collective professional experience, responses to a standardized questionnaire, and serial discussions of wide‐ranging issues related to Glut1DS. Key clinical features signaling the onset of Glut1DS are eye‐head movement abnormalities, seizures, neurodevelopmental impairment, deceleration of head growth, and movement disorders. Diagnosis is confirmed by the presence of these clinical signs, hypoglycorrhachia documented by lumbar puncture, and genetic analysis showing pathogenic SLC2A1 variants. KDT represent standard choices with Glut1DS‐specific recommendations regarding duration, composition, and management. Ongoing research has identified future interventions to restore Glut1 protein content and function. Clinical manifestations are influenced by patient age, genetic complexity, and novel therapeutic interventions. All clinical phenotypes will benefit from a better understanding of Glut1DS natural history throughout the life cycle and from improved guidelines facilitating early diagnosis and prompt treatment. Often, the presenting seizures are treated initially with antiseizure drugs before the cause of the epilepsy is ascertained and appropriate KDT are initiated. Initial drug treatment fails to treat the underlying metabolic disturbance during early brain development, contributing to the long‐term disease burden. Impaired development of the brain microvasculature is one such complication of delayed Glut1DS treatment in the postnatal period. This international consensus statement should facilitate prompt diagnosis and guide best standard of care for Glut1DS throughout the life cycle.
Developmental and epileptic encephalopathies (DEEs) can be primarily attributed to genetic causes. The genetic landscape of DEEs has been largely shaped by the rise of high-throughput sequencing, which led to the discovery of new DEE-associated genes and helped identify de novo pathogenic variants. We discuss briefly the contribution of de novo variants to DEE and also focus on alternative inheritance models that contribute to DEE. First, autosomal recessive inheritance in outbred populations may have a larger contribution than previously appreciated, accounting for up to 13% of DEEs. A small subset of genes that typically harbor de novo variants have been associated with recessive inheritance, and often these individuals have more severe clinical presentations. Additionally, pathogenic variants in X-linked genes have been identified in both affected males and females, possibly due to a lack of X-chromosome inactivation skewing. Collectively, exome sequencing has resulted in a molecular diagnosis for many individuals with DEE, but this still leaves many cases unsolved. Multiple factors contribute to the missing etiology, including nonexonic variants, mosaicism, epigenetics, and oligogenic inheritance. Here, we focus on the first 2 factors. We discuss the promises and challenges of genome sequencing, which allows for a more comprehensive analysis of the genome, including interpretation of structural and noncoding variants and also yields a high number of de novo variants for interpretation. We also consider the contribution of genetic mosaicism, both what it means for a molecular diagnosis in mosaic individuals and the important implications for genetic counseling.
Epilepsy is common in early childhood. In this age group it is associated with high rates of therapy-resistance, and with cognitive, motor, and behavioural comorbidity. A large number of genes, with wide ranging functions, are implicated in its aetiology, especially in those with therapy-resistant seizures. Identifying the more common single-gene epilepsies will aid in targeting resources, the prioritization of diagnostic testing and development of precision therapy. Previous studies of genetic testing in epilepsy have not been prospective and population-based. Therefore, the population-incidence of common genetic epilepsies remains unknown. The objective of this study was to describe the incidence and phenotypic spectrum of the most common single-gene epilepsies in young children, and to calculate what proportion are amenable to precision therapy. This was a prospective national epidemiological cohort study. All children presenting with epilepsy before 36 months of age were eligible. Children presenting with recurrent prolonged (>10 min) febrile seizures; febrile or afebrile status epilepticus (>30 min); or with clusters of two or more febrile or afebrile seizures within a 24-h period were also eligible. Participants were recruited from all 20 regional paediatric departments and four tertiary children's hospitals in Scotland over a 3-year period. DNA samples were tested on a custom-designed 104-gene epilepsy panel. Detailed clinical information was systematically gathered at initial presentation and during follow-up. Clinical and genetic data were reviewed by a multidisciplinary team of clinicians and genetic scientists. The pathogenic significance of the genetic variants was assessed in accordance with the guidelines of UK Association of Clinical Genetic Science (ACGS). Of the 343 patients who met inclusion criteria, 333 completed genetic testing, and 80/333 (24%) had a diagnostic genetic finding. The overall estimated annual incidence of single-gene epilepsies in this well-defined population was 1 per 2120 live births (47.2/100 000; 95% confidence interval 36.9-57.5). PRRT2 was the most common single-gene epilepsy with an incidence of 1 per 9970 live births (10.0/100 000; 95% confidence interval 5.26-14.8) followed by SCN1A: 1 per 12 200 (8.26/100 000; 95% confidence interval 3.93-12.6); KCNQ2: 1 per 17 000 (5.89/100 000; 95% confidence interval 2.24-9.56) and SLC2A1: 1 per 24 300 (4.13/100 000; 95% confidence interval 1.07-7.19). Presentation before the age of 6 months, and presentation with afebrile focal seizures were significantly associated with genetic diagnosis. Single-gene disorders accounted for a quarter of the seizure disorders in this cohort. Genetic testing is recommended to identify children who may benefit from precision treatment and should be mainstream practice in early childhood onset epilepsy.
Purpose:
Dravet syndrome (DS) is a well-described, severe genetic epileptic encephalopathy with an increased risk of SUDEP. The incidence and genetic architecture of DS in African patients is virtually unknown, largely due to lack of awareness and unavailability of genetic testing. The clinical benefits of the available precision medicine approaches to treatment emphasise the importance of an early, correct diagnosis. We investigated the genetic causes and clinical features of DS in South African children to develop protocols for early, cost-effective diagnosis in the local setting.
Method:
We selected 22 South African children provisionally diagnosed with clinical DS for targeted resequencing of DS-associated genes. We sought to identify the clinical features most strongly associated with SCN1A-related DS, using the DS risk score and clinical co-variates under various statistical models.
Results:
Disease-causing variants were identified in 10 of the 22 children: nine SCN1A and one PCDH19. Moreover, we showed that seizure onset before 6 months of age and a clinical DS risk score of >6 are highly predictive of SCN1A-associated DS. Clinical reassessment resulted in a revised diagnosis in 10 of the 12 variant-negative children.
Conclusion:
This first genetic study of DS in Africa confirms that de novo SCN1A variants underlie disease in the majority of South African patients. Affirming the predictive value of seizure onset before 6 months of age and a clinical DS risk score of >6 has significant practical implications for the resource-limited setting, presenting simple diagnostic criteria which can facilitate early correct treatment, specialist consultation and genetic testing.
Objective
Pathogenic variants in SCN1A can give rise to extremely variable disease severities that may be indistinguishable at their first presentation. We aim to find clinical features that can help predict the evolution of seizures into Dravet syndrome and clinical features that predict cognitive outcome in Dravet syndrome. We specifically investigate the role of contraindicated medication (CIM) as a possible modifier of cognitive decline.
Methods
A cohort of 164 Dutch participants with SCN1A‐related seizures was evaluated. Clinical data were collected from medical records and semistructured telephone interviews. Cognitive function was classified by a child neurologist, neuropsychologist, and clinical geneticist. Several clinical variables, including duration of CIM use in the first 5 years of disease, were evaluated in univariate and multivariate analyses.
Results
A longer duration of CIM use in the first 5 years after seizure onset was significantly associated with a worse cognitive outcome at time of inclusion, and with lower interpolated intelligence quotient/developmental quotient scores after the first 5 years of disease in Dravet syndrome patients. CIM use remained a significant predictor for cognitive outcome in a multivariate regression model, as did age at the first observation of developmental delay and age at first afebrile seizure. Age at first afebrile seizure was the most accurate predictor for evolution of seizures into Dravet syndrome for the complete cohort.
Significance
Our data suggest that a longer CIM use in the first 5 years of disease can have negative effects on cognitive outcome in Dravet syndrome. An early diagnosis is essential to avoid these drugs. Furthermore, we identified age at first afebrile seizure as an important predictor for evolution of seizures into Dravet syndrome and for the severity of Dravet syndrome, which can be used to counsel parents of young patients with SCN1A‐related seizures.
Objective
The severe epilepsies of infancy (SEI) are a devastating group of disorders that pose a major care and economic burden on society; early diagnosis is critical for optimal management. This study sought to determine the incidence and etiologies of SEI, and model the yield and cost‐effectiveness of early genetic testing.
Methods
A population‐based study was undertaken of the incidence, etiologies, and cost‐effectiveness of a whole exome sequencing–based gene panel (targeted WES) in infants with SEI born during 2011‐2013, identified through electroencephalography (EEG) and neonatal databases. SEI was defined as seizure onset before age 18 months, frequent seizures, epileptiform EEG, and failure of ≥2 antiepileptic drugs. Medical records, investigations, MRIs, and EEGs were analyzed, and genetic testing was performed if no etiology was identified. Economic modeling was performed to determine yield and cost‐effectiveness of investigation of infants with unknown etiology at epilepsy onset, incorporating targeted WES at different stages of the diagnostic pathway.
Results
Of 114 infants with SEI (incidence = 54/100 000 live births/y), the etiology was determined in 76 (67%): acquired brain injuries (n = 14), focal cortical dysplasias (n = 14), other brain malformations (n = 17), channelopathies (n = 11), chromosomal (n = 9), metabolic (n = 6), and other genetic (n = 5) disorders. Modeling showed that incorporating targeted WES increased diagnostic yield compared to investigation without targeted WES (48/86 vs 39/86). Early targeted WES had lower total cost (738 136 USD) than late targeted WES. A pathway with early targeted WES and limited metabolic testing yielded 7 additional diagnoses compared to investigation without targeted WES (46/86 vs 39/86), with lower total cost (661 103 USD), lower cost per diagnosis (16 951 USD), and a dominant cost‐effectiveness ratio.
Significance
Severe epilepsies occur in 1 in 2000 infants, with the etiology identified in two‐thirds, most commonly malformative. Early use of targeted WES yields more diagnoses at lower cost. Early genetic diagnosis will enable timely administration of precision medicines, once developed, with the potential to improve long‐term outcome.
Over 80% of people with epilepsy live in low- to middle-income countries where epilepsy is often undiagnosed and untreated due to limited resources and poor infrastructure. In Africa, the burden of epilepsy is exacerbated by increased risk factors such as central nervous system infections, perinatal insults, and traumatic brain injury. Despite the high incidence of these etiologies, the cause of epilepsy in over 60% of African children is unknown, suggesting a possible genetic origin. Large-scale genetic and genomic research in Europe and North America has revealed new genes and variants underlying disease in a range of epilepsy phenotypes. The relevance of this knowledge to patient care is especially evident among infants with early-onset epilepsies, where early genetic testing can confirm the diagnosis and direct treatment, potentially improving prognosis and quality of life. In Africa, however, genetic epilepsies are among the most under-investigated neurological disorders, and little knowledge currently exists on the genetics of epilepsy among African patients. The increased diversity on the continent may yield unique, important epilepsy-associated genotypes, currently absent from the North American or European diagnostic testing protocols. In this review, we propose that there is strong justification for developing the capacity to offer genetic testing for children with epilepsy in Africa, informed mostly by the existing counseling and interventional needs. Initial simple protocols involving well-recognized epilepsy genes will not only help patients but will give rise to further clinically relevant research, thus increasing knowledge and capacity.
PurposeThe 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines were a major step toward establishing a common framework for variant classification. In practice, however, several aspects of the guidelines lack specificity, are subject to varied interpretations, or fail to capture relevant aspects of clinical molecular genetics. A simple implementation of the guidelines in their current form is insufficient for consistent and comprehensive variant classification.Methods
We undertook an iterative process of refining the ACMG-AMP guidelines. We used the guidelines to classify more than 40,000 clinically observed variants, assessed the outcome, and refined the classification criteria to capture exceptions and edge cases. During this process, the criteria evolved through eight major and minor revisions.ResultsOur implementation: (i) separated ambiguous ACMG-AMP criteria into a set of discrete but related rules with refined weights; (ii) grouped certain criteria to protect against the overcounting of conceptually related evidence; and (iii) replaced the "clinical criteria" style of the guidelines with additive, semiquantitative criteria.Conclusion
Sherloc builds on the strong framework of 33 rules established by the ACMG-AMP guidelines and introduces 108 detailed refinements, which support a more consistent and transparent approach to variant classification.GENETICS in MEDICINE advance online publication, 11 May 2017; doi:10.1038/gim.2017.37.
Disclaimer: These ACMG Standards and Guidelines were developed primarily as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory services. Adherence to these standards and guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the clinical laboratory geneticist should apply his or her own professional judgment to the specific circumstances presented by the individual patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient’s record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these Standards and Guidelines. They also are advised to take notice of the date any particular guideline was adopted and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.
The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.¹ In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes, and epigenetic assays for genetic disorders. By virtue of increased complexity, this shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context the ACMG convened a workgroup in 2013 comprising representatives from the ACMG, the Association for Molecular Pathology (AMP), and the College of American Pathologists to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP, and College of American Pathologists stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories, including genotyping, single genes, panels, exomes, and genomes. This report recommends the use of specific standard terminology—“pathogenic,” “likely pathogenic,” “uncertain significance,” “likely benign,” and “benign”—to describe variants identified in genes that cause Mendelian disorders. Moreover, this recommendation describes a process for classifying variants into these five categories based on criteria using typical types of variant evidence (e.g., population data, computational data, functional data, segregation data). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a Clinical Laboratory Improvement Amendments–approved laboratory, with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or the equivalent.
Genet Med17 5, 405–423.
The investigation of children presenting with infantile and childhood epileptic encephalopathies (ICEE) is challenging due to diverse aetiologies, overlapping phenotypes and the relatively low diagnostic yield of MRI, electroencephalography (EEG) and biochemical investigations. Careful history and thorough examination remain essential as these may identify an acquired cause or indicate more targeted investigation for a genetic disorder. Whole exome sequencing (WES) with analysis of a panel of candidate epilepsy genes has increased the diagnostic yield. Whole genome sequencing (WGS), particularly as a trio with both parents’ DNA, is likely to supersede WES. Modern genomic investigation impacts on the timing and necessity of other testing. We propose a structured approach for children presenting with ICEE where there is diagnostic uncertainty, emphasising the importance of WGS or, if unavailable, WES early in the investigative process. We note the importance of expert review of all investigations, including radiology, neurophysiology and biochemistry, to confirm the technique used was appropriate as well as the results. It is essential to counsel families on the risks associated with the procedures, the yield of the procedures, findings that are difficult to interpret and implication of ‘negative’ results. Where children remain without a diagnosis despite comprehensive investigation, we note the importance of ongoing multidisciplinary care.
The recent introduction of the term 'developmental and epileptic encephalopathy' by the International League Against Epilepsy has added another conceptual layer to understanding the most severe group of epilepsies. An epileptic encephalopathy is defined by the presence of frequent epileptiform activity that impacts adversely on development, typically causing slowing or regression of developmental skills, and usually associated with frequent seizures. Many of the epileptic encephalopathies are now known to have an identifiable molecular genetic basis. The term 'developmental' was introduced as there are multiple facets leading to developmental impairment in affected individuals. The underlying genetic cause often results in developmental delay in its own right, with the epileptic encephalopathy further adversely affecting development. Treatment of the epileptic encephalopathy may improve developmental progress, so early recognition and active management are essential to improve developmental outcomes. Equally, understanding that the genetic aetiology independently leads to developmental impairment means that precision therapies need to be holistic in addressing the devastating consequences of this group of diseases.
Background:
The advent of Next Generation Sequencing (NGS) has led to a redefining of the genetic landscape of the epilepsies. Hundreds of single gene epilepsies have been described. Genes associated with epilepsy involve diverse processes. Now a substantial proportion of individuals with epilepsy can receive a high definition molecular genetic diagnosis.
Methods:
In this review we update the current genetic landscape of the epilepsies and categorise the major functional groupings of epilepsy-associated genes. We describe currently available genetic testing approaches. We perform a literature review of NGS studies and review the factors which determine yield in cohorts undergoing testing. We identify factors associated with positive genetic diagnosis and consider the utility of genetic testing in terms of treatment selection as well as more qualitative aspects of care.
Findings:
Epilepsy-associated genes can be grouped into five broad functional categories: ion transport; cell growth and differentiation; regulation of synaptic processes; transport and metabolism of small molecules within and between cells; and regulation of gene transcription and translation. Early onset of seizures, drug-resistance, and developmental comorbidity are associated with higher diagnostic yield. The most commonly implicated genes in NGS studies to date, in order, are SCN1A, KCNQ2, CDKL5, SCN2A, and STXBP1. In unselected infantile cohorts PRRT2, a gene associated with self-limited epilepsy, is frequently implicated. Genetic diagnosis provides utility in terms of treatment choice closing the diagnostic odyssey, avoiding unnecessary further testing, and informing future reproductive decisions.
Conclusions:
Genetic testing has become a first line test in epilepsy. As techniques improve and understanding advances, its utility is set to increase. Genetic diagnosis, particularly in early onset developmental and epileptic encephalopathies, influences treatment choice in a significant proportion of patients. The realistic prospect of gene therapy is a cause for optimism.
Dravet syndrome is a rare but severe epilepsy syndrome that begins in the first year of life with recurrent seizures triggered by fever that are typically prolonged and hemiclonic. The epilepsy is highly drug resistant. Although development is normal at onset, over time, most patients develop moderate-to-severe intellectual disability, behavior disorders, and a characteristic crouch gait. There is a significant mortality, predominantly owing to sudden unexpected death in epilepsy. Complete seizure control is rarely attainable. Initial therapy includes valproic acid and clobazam, but response is typically inadequate. The results of new drugs for Dravet syndrome, including stiripentol, cannabidiol, and fenfluramine, are very promising. Stiripentol was associated with a greater than 50% reduction in convulsive seizure frequency in 71% of cases, when added to valproic acid and clobazam, and also markedly reduced status epilepticus. Pharmaceutical-grade cannabidiol resulted in a median change in monthly motor seizures from baseline of − 36.5%. Fenfluramine was associated with a greater than 50% reduction in seizures of 70%, with one quarter of cases achieving near seizure freedom over the duration of the trial. These agents are generally well tolerated, with few patients discontinuing for adverse effects. There is limited evidence to date regarding improvement in cognition with these newer agents; however, a meaningful change is challenging to assess over short trial periods and requires longer follow-up studies. While current treatments focus predominantly on seizure control, newer therapies including genetic treatments and antisense oligonucleotides can target the SCN1A channelopathy, and thus, may also significantly impact the important co-morbidities associated with this syndrome.
Background:
KCNQ2 related disorders comprise both benign seizure disorders and early onset epileptic encephalopathies. Especially within the latter group, patients suffer from refractory seizures to standard antiepileptic drugs and developmental delay. Besides the hope of personalized medical approaches to treat the recently unraveled large amount of genetic channelopathies, there are sparse systematic data on treatment responses in KCNQ2 related epilepsy in larger cohorts.
Methods:
We searched PubMed using the free text term search 'KCNQ2 AND Epilepsy' and identified additional records using PubMed Medical Subject Headings (MeSH). Based on patients' clinical information about their therapy they were assigned to one of four groups: 'seizure freedom', 'responder', 'successful therapy', and 'unsuccessful therapy'.
Results:
Out of 52 studies, 217 subjects were eligible for further data analyses. 133 patients were classified as 'benign' seizure disorders whereas 84 patients were classified as 'Early Onset Epileptic Encephalopathy (EOEE)'. In the 'benign' group, 92.5% of patients became seizure free while 3.8% did not respond to treatment. In contrast 65.5% of patients in the 'EOEE' group were reported seizure free, while 14.3% showed no treatment success (p = 0.003). Spontaneous seizure remission (without medication) was 30.1% in the 'benign' group. Phenobarbital and sodium channel blockers most often lead to seizure freedom in patients with a 'benign' course. In patients with 'EOEE' seizure freedom was more likely achieved when receiving sodium channel blockers.
Conclusions:
Seizures associated with mutations within the voltage gated potassium channel KCNQ2 are well controlled by medical treatment in patients with 'benign' courses and moderately well in patients with the 'EOEE' group. A significant number of patients in the 'benign' group may experience seizure freedom spontaneously. Phenobarbital might be considered in benign courses, while sodium channel blockers seem appropriate for both 'benign' and 'EOEE' patients.
Importance
Clinical genomic tests that examine the DNA sequence of large numbers of genes are commonly used in the diagnosis and management of epilepsy in pediatric patients. The permanence of genomic test result interpretations is not known.
Objective
To investigate the value of reinterpreting previously reported genomic test results.
Design, Setting, and Participants
This study retrospectively reviewed and reinterpreted genomic test results from July 1, 2012, to August 31, 2015, for pediatric patients who previously underwent genomic epilepsy testing at a single tertiary care pediatric health care facility. Reinterpretation of previously reported variants was conducted in May 2017.
Main Outcomes and Measures
Patient reports from clinical genomic epilepsy tests were reviewed, and all reported genetic variants were reinterpreted using 2015 consensus standards and guidelines for interpreting hereditary genetic variants. Three classification tiers were used in the reinterpretation: pathogenic or likely pathogenic variant, variant of uncertain significance (VUS), or benign or likely benign variant.
Results
A total of 309 patients had genomic epilepsy tests performed (mean [SD] age, 5.6 [0.8] years; 163 [52.8%] male), and 185 patients had a genetic variant reported. The reported variants resulted in 61 patients with and 124 patients without a genetic diagnosis (VUS variants only). On reinterpretation of all reported variants, 67 of the 185 patients (36.2%) had a change in variant classification. Of the 67 patients with a genetic variant change in interpretation, 21 (31.3%) experienced a change in diagnosis. During the 5 years of the study, 19 of 61 patients (31.1%) with a genetic diagnosis and 48 of 124 patients (38.7%) with undiagnosed conditions (VUS only) had their results reclassified. Review of genomic reports issued during the final 2 years of the study identified reclassification of variants in 4 of 16 patients (25.0%) with a pathogenic or likely pathogenic variant and 11 of 41 patients (26.8%) with a VUS.
Conclusions and Relevance
The identified high rate of reinterpretation in this study suggests that interpretation of genomic test results has rapidly evolved during the past 5 years. These findings suggest that reinterpretation of genomic test results should be performed at least every 2 years.
Objective:
To characterize the features associated with PCDH19-related epilepsy, also known as "female-limited epilepsy."
Methods:
We analyzed data from participants enrolled in the PCDH19 Registry, focusing on the seizure-related, developmental, neurobehavioral, and sleep-related features. We evaluated variants for pathogenicity based on previous reports, population databases, and in silico predictions, and included individuals with pathogenic or potentially pathogenic variants. We performed a retrospective analysis of medical records and administered a targeted questionnaire to characterize current or past features in probands and genotype-positive family members.
Results:
We included 38 individuals with pathogenic or potentially pathogenic variants in PCDH19: 21 de novo, 5 maternally inherited, 7 paternally inherited, and 5 unknown. All 38 had epilepsy; seizure burden varied, but typical features of clustering of seizures and association with fever were present. Thirty individuals had intellectual disability (ID), with a wide range of severity reported; notably, 8/38 (22%) had average intellect. Behavioral and sleep dysregulation were prominent, in 29/38 (76%) and 20/38 (53%), respectively. Autistic features were present in 22/38 (58%), of whom 12 had a formal diagnosis of autism spectrum disorder. We had additional data from 5 genotype-positive mothers, all with average intellect and 3 with epilepsy, and from 1 genotype-positive father.
Significance:
Our series represents a robust cohort with carefully curated PCDH19 variants. We observed seizures as a core feature with a range of seizure types and severity. Whereas the majority of individuals had ID, we highlight the possibility of average intellect in the setting of PCDH19-related epilepsy. We also note the high prevalence and severity of neurobehavioral phenotypes associated with likely pathogenic variants in PCDH19. Sleep dysregulation was also a major area of concern. Our data emphasize the importance of appropriate referrals for formal neuropsychological evaluations as well as the need for formal prospective studies to characterize the PCDH19-related neurodevelopmental syndrome in children and their genotype-positive parents.
Objective:
Pathogenic variants involving the CDKL5 gene result in a severe epileptic encephalopathy, often later presenting with features similar to Rett syndrome. Cardinal features of epilepsy in the CDKL5 disorder include early onset at a median age of 6 weeks and poor response to antiepileptic drugs. The ketogenic diet (KD) was first introduced in the 1920s as a treatment option for refractory epilepsy in children. This study investigated use of the KD in the CDKL5 disorder and its influences on seizures.
Methods:
The International CDKL5 Disorder Database, established in 2012, collects information on individuals with the CDKL5 disorder. Families have provided information regarding seizure characteristics, use, and side effects of the KD treatment. Descriptive statistics and time to event analyses were performed. Clinical vignettes were also provided on patients attending Boston Children's Hospital.
Results:
Data regarding KD use were available for 204 individuals with a pathogenic CDKL5 variant. Median age of inclusion in the database was 4.8 years (range = 0.3-33.9 years), with median age of 6 weeks (range = 1 day-65 weeks) at seizure onset. History of KD use was reported for 51% (104 of 204) of individuals, with a median duration of use of 17 months (95% confidence interval = 9-24). Changes in seizure activity after commencing KD were reported for two-thirds (69 of 104), with improvements in 88% (61 of 69). Nearly one-third (31.7%) experienced side effects during the diet. At ascertainment, only one-third (32%) remained on the diet, with lack of long-term efficacy as the main reason for diet cessation (51%, 36 of 70).
Significance:
Benefits of KD in the CDKL5 disorder are in keeping with previous trials on refractory epilepsies. However, poor long-term efficacy remains as a significant barrier. In view of its side effect profile, KD administration should be supervised by a pediatric neurologist and specialist dietician.
Purpose:
PCDH19 mutations cause epilepsy and mental retardation limited to females (EFMR) or Dravet-like syndromes. Especially in the first years of life, epilepsy is known to be highly pharmacoresistant. The aim of our study was to evaluate the effectiveness of antiepileptic therapy in patients with PCDH19 mutations.
Methods:
We report a retrospective multicenter study of antiepileptic therapy in 58 female patients with PCDH19 mutations and epilepsy aged 2-27 years (mean age 10.6 years).
Results:
The most effective drugs after 3 months were clobazam and bromide, with a responder rate of 68% and 67%, respectively, where response was defined as seizure reduction of at least 50%. Defining long-term response as the proportion of responders after 12 months of treatment with a given drug in relation to the number of patients treated for at least 3 months, the most effective drugs after 12 months were again bromide and clobazam, with a long-term response of 50% and 43%, respectively. Seventy-four percent of the patients became seizure-free for at least 3 months, 47% for at least one year.
Significance:
The most effective drugs in patients with PCDH19 mutations were bromide and clobazam. Although epilepsy in PCDH19 mutations is often pharmacoresistant, three quarters of the patients became seizure-free for at least for 3 months and half of them for at least one year. However, assessing the effectiveness of the drugs is difficult because a possible age-dependent spontaneous seizure remission must be considered.
Despite the diversity of the African population, genetic studies, of epilepsy in particular, have been limited, especially in sub-Saharan Africa. In recent years, with the regression of infectious diseases in developing countries, the focus has shifted more towards non communicable disorders. The prevalence of epilepsy in Africa is higher compared to other continents. Although this has been attributed to the high rate of infectious diseases, genetic contributions should not be ignored. Research in genetic epilepsy in Africa could well benefit from the decreasing cost of genetic analysis, and could contribute to further our knowledge on the spectrum of these diseases in Africa. The growing collaboration between African research institutions and those of developed countries offers a unique opportunity to boost research in Africa and improve our global understanding of human disease, thus leading to the development of better therapeutic approaches.
Recent progress in genetic testing has facilitated obtaining an etiologic diagnosis in children with developmental delay/intellectual disability (DD/ID) or multiple congenital anomalies (MCA) or both. Little is known about the benefits of diagnostic elucidation for affected families. We studied the impact of a genetic diagnosis on parental quality of life (QoL) using a validated semiquantitative questionnaire in families with a disabled child investigated by array CGH. We received completed questionnaires from 95 mothers and 76 fathers of 99 families. We used multivariate analysis for adjustment of potential confounders. Taken all 99 families together maternal QoL score (percentile rank scale 51.05) was significantly lower than fathers' QoL (61.83, p = 0.01). Maternal QoL score was 20.17 (95% CI [5.49; 34.82]) percentile rank scales higher in mothers of children with diagnostic (n = 34) array CGH as opposed to mothers of children with inconclusive (n = 65) array CGH (Hedges' g 0,71). Comparison of these QoL scores with retrospectively recalled QoL before array CGH revealed an increase of maternal QoL after diagnostic clarification. Our results indicate a benefit for maternal QoL if a genetic test, here array CGH, succeeds to clarify the etiologic diagnosis in a disabled child.
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Objective
Epilepsy is a common neurologic disorder of childhood. To determine the genetic diagnostic yield in epileptic encephalopathy, we performed a retrospective cohort study in a single epilepsy genetics clinic.Methods
We included all patients with intractable epilepsy, global developmental delay, and cognitive dysfunction seen between January 2012 and June 2014 in the Epilepsy Genetics Clinic. Electronic patient charts were reviewed for clinical features, neuroimaging, biochemical investigations, and molecular genetic investigations including targeted next-generation sequencing of epileptic encephalopathy genes.ResultsGenetic causes were identified in 28% of the 110 patients: 7% had inherited metabolic disorders including pyridoxine dependent epilepsy caused by ALDH7A1 mutation, Menkes disease, pyridox(am)ine-5-phosphate oxidase deficiency, cobalamin G deficiency, methylenetetrahydrofolate reductase deficiency, glucose transporter 1 deficiency, glycine encephalopathy, and pyruvate dehydrogenase complex deficiency; 21% had other genetic causes including genetic syndromes, pathogenic copy number variants on array comparative genomic hybridization, and epileptic encephalopathy related to mutations in the SCN1A, SCN2A, SCN8A, KCNQ2, STXBP1, PCDH19, and SLC9A6 genes. Forty-five percent of patients obtained a genetic diagnosis by targeted next-generation sequencing epileptic encephalopathy panels. It is notable that 4.5% of patients had a treatable inherited metabolic disease.SignificanceTo the best of our knowledge, this is the first study to combine inherited metabolic disorders and other genetic causes of epileptic encephalopathy. Targeted next-generation sequencing panels increased the genetic diagnostic yield from <10% to >25% in patients with epileptic encephalopathy.
We analyzed by next-generation sequencing (NGS) 67 epilepsy genes in 19 patients with different types of either isolated or syndromic epileptic disorders and in 15 controls to investigate whether a quick and cheap molecular diagnosis could be provided. The average number of nonsynonymous and splice site mutations per subject was similar in the two cohorts indicating that, even with relatively small targeted platforms, finding the disease gene is not an univocal process. Our diagnostic yield was 47% with nine cases in which we identified a very likely causative mutation. In most of them no interpretation would have been possible in absence of detailed phenotype and familial information. Seven out of 19 patients had a phenotype suggesting the involvement of a specific gene. Disease-causing mutations were found in six of these cases. Among the remaining patients, we could find a probably causative mutation only in three. None of the genes affected in the latter cases had been suspected a priori. Our protocol requires 8-10 weeks including the investigation of the parents with a cost per patient comparable to sequencing of 1-2 medium-to-large-sized genes by conventional techniques. The platform we used, although providing much less information than whole-exome or whole-genome sequencing, has the advantage that can also be run on 'benchtop' sequencers combining rapid turnaround times with higher manageability.European Journal of Human Genetics advance online publication, 21 May 2014; doi:10.1038/ejhg.2014.92.
During the past 2 years, next-generation DNA sequencing (NGS) has become a widespread diagnostic tool in neurology. Several studies have addressed the diagnostic yield and cost of NGS relative to other types of DNA testing. G-banded karyotyping identifies chromosomal aberrations and has a 3% diagnostic yield for unexplained developmental disabilities or other congenital anomalies.¹ In comparison, chromosomal microarrays detect gene copy number variations and have a yield of 15% to 20% for the same disorder categories.¹ Next-generation DNA sequencing, in the format of whole-exome sequencing (WES), can be diagnostic in 25% of neurogenetic cases.² Similarly, whole-genome sequencing (WGS) with NGS has a reported diagnostic yield of 27% in children and adults with a broad variety of diseases.³ In contrast to WES and WGS, targeted NGS panels focus on subsets (dozens to hundreds) of genes associated with specific phenotypes. For example, targeted NGS directed at a single disease category, such as congenital glycosylation disorders, has a reported diagnostic yield of 14.8%.⁴ Given the prevalence of pediatric epilepsy, we set out to critically assess the diagnostic yield of an NGS panel for epilepsy in a pediatric tertiary care hospital.
In 2012, 28 patients were tested using either the GeneDx Comprehensive or the Infantile Epilepsy Gene Panels. Six patients harbored pathogenic or likely pathogenic mutations in 5 epilepsy-associated genes (TCF4, SCN1A, CDKL5, KCNQ2, and POLG) and 11 patients were found to have novel missense variants that were classified as variants of unknown significance in 8 genes (GABRG2, MECP2, PNPO, SCN1A, SCN2A, SCN1B, SLC9A6, and TSC2). All of the pathogenic mutations had been previously characterized as such in the literature; novel variants that were likely pathogenic were reported as variants of unknown significance. The diagnostic yield of these disease-targeted NGS panels was 21.4% (6 of 28 patients), on par with WES or WGS.²- 4 If the GeneDx criteria for prior reporting in diagnosing pathogenicity had been used in a recent study of clinical WES, the WES diagnostic yield would have been only 18%²; therefore, with equivalent reporting criteria, these NGS panel tests for epilepsy would have a superior diagnostic yield compared with WES.
Understanding the aetiology of epilepsy is essential both for clinical management of patients and for conducting neurobiological research that will direct future therapies. The aetiology of epilepsy was formerly regarded as unknown in about three-quarters of patients; however, massively parallel gene-sequencing studies, conducted in a framework of international collaboration, have yielded a bounty of discoveries that highlight the importance of gene mutations in the aetiology of epilepsy. These data, coupled with clinical genetic studies, suggest a new paradigm for use in the clinic: many forms of epilepsy are likely to have a genetic basis. Enquiry about a genetic cause of epilepsy is readily overlooked in the clinic for a number of understandable but remediable reasons, not least an incomplete understanding of its genetic architecture. In addition, the importance of de novo mutagenesis is often underappreciated, particularly in the epileptic encephalopathies. Other genomic surprises are worth emphasizing, such as the emerging evidence of a genetic contribution to focal epilepsies-long regarded as acquired conditions-and the complex role of copy number variation. The importance of improved understanding of the genetics of the epilepsies is confirmed by the positive outcomes, in terms of treatment selection and counselling, of receiving a genetic diagnosis.
Aim Genetic testing in the epilepsies is becoming an increasingly accessible clinical tool. Mutations in the sodium channel alpha 1 subunit (SCN1A) gene are most notably associated with Dravet syndrome. This is the first study to assess the impact of SCN1A testing on patient management from both carer and physician perspectives.
Method Participants were identified prospectively from referrals to the Epilepsy Genetics Service in Glasgow and contacted via their referring clinicians. Questionnaires exploring the consequences of SCN1A genetic testing for each case were sent to carers and physicians.
Results Of the 244 individuals contacted, 182 (75%) carried a SCN1A mutation. Carers of 187 (77%) patients responded (90 females, 97 males; mean age at referral 4y 10mo; interquartile range 9y 1mo). Of those participants whose children tested positive for a mutation, 87% reported that genetic testing was helpful, leading to treatment changes resulting in fewer seizures and improved access to therapies and respite care. Out of 187 physicians, 163 responded (87%), of whom 48% reported that a positive test facilitated diagnosis earlier than with clinical and electroencephalography data alone. It prevented additional investigations in 67% of patients, altered treatment approach in 69%, influenced medication choice in 74%, and, through medication change, improved seizure control in 42%.
Interpretation In addition to confirming a clinical diagnosis, a positive SCN1A test result influenced treatment choice and assisted in accessing additional therapies, especially in the very young.
Epilepsies have a highly heterogeneous background with a strong genetic contribution. The variety of unspecific and overlapping syndromic and nonsyndromic phenotypes often hampers a clear clinical diagnosis and prevents straightforward genetic testing. Knowing the genetic basis of a patient's epilepsy can be valuable not only for diagnosis but also for guiding treatment and estimating recurrence risks.
To overcome these diagnostic restrictions, we composed a panel of genes for Next Generation Sequencing containing the most relevant epilepsy genes and covering the most relevant epilepsy phenotypes known so far. With this method, 265 genes were analyzed per patient in a single step. We evaluated this panel on a pilot cohort of 33 index patients with concise epilepsy phenotypes or with a severe but unspecific seizure disorder covering both sporadic and familial cases.
We identified presumed disease-causing mutations in 16 of 33 patients comprising sequence alterations in frequently as well as in less commonly affected genes. The detected aberrations encompassed known and unknown point mutations (SCN1A p.R222X, p. E289V, p.379R, p.R393H; SCN2A p.V208E; STXBP1 p.R122X; KCNJ10 p.L68P, p.I129V; KCTD7 p.L108M; KCNQ3 p.P574S; ARHGEF9 p.R290H; SMS p.F58L; TPP1 p.Q278R, p.Q422H; MFSD8 p.T294K), a putative splice site mutation (SCN1A c.693A> p.T/P231P) and small deletions (SCN1A p.F1330Lfs3X [1 bp]; MFSD8 p.A138Dfs10X [7 bp]). All mutations have been confirmed by conventional Sanger sequencing and, where possible, validated by parental testing and segregation analysis. In three patients with either Dravet syndrome or myoclonic epilepsy, we detected SCN1A mutations (p.R222X, p.P231P, p.R393H), even though other laboratories had previously excluded aberrations of this gene by Sanger sequencing or high-resolution melting analysis.
We have developed a fast and cost-efficient diagnostic screening method to analyze the genetic basis of epilepsies. We were able to detect mutations in patients with clear and with unspecific epilepsy phenotypes, to uncover the genetic basis of many so far unresolved cases with epilepsy including mutation detection in cases in which previous conventional methods yielded falsely negative results. Our approach thus proved to be a powerful diagnostic tool that may contribute to collecting information on both common and unknown epileptic disorders and in delineating associated phenotypes of less frequently mutated genes.
In this report, the International League Against Epilepsy (ILAE) Genetics Commission discusses essential issues to be considered with regard to clinical genetic testing in the epilepsies. Genetic research on the epilepsies has led to the identification of more than 20 genes with a major effect on susceptibility to idiopathic epilepsies. The most important potential clinical application of these discoveries is genetic testing: the use of genetic information, either to clarify the diagnosis in people already known or suspected to have epilepsy (diagnostic testing), or to predict onset of epilepsy in people at risk because of a family history (predictive testing). Although genetic testing has many potential benefits, it also has potential harms, and assessment of these potential benefits and harms in particular situations is complex. Moreover, many treating clinicians are unfamiliar with the types of tests available, how to access them, how to decide whether they should be offered, and what measures should be used to maximize benefit and minimize harm to their patients. Because the field is moving rapidly, with new information emerging practically every day, we present a framework for considering the clinical utility of genetic testing that can be applied to many different syndromes and clinical contexts. Given the current state of knowledge, genetic testing has high clinical utility in few clinical contexts, but in some of these it carries implications for daily clinical practice.
Communication with parents who are realizing their child is severely disabled is a difficult task for professionals. Parents are experiencing great emotional stress during the diagnostic process and dissatisfaction with disclosure is widespread. The aim of this study was to investigate parents' reactions when realizing their child's disability, the impact of the diagnosis and parents' ways of coping.
This was a qualitative, longitudinal study, using in-depth interviews with 16 parents of a physically and mentally disabled child who had recently been diagnosed as such. Children's age at inclusion ranged from 1 to 27 months. Half of the children had an unknown diagnosis. Data were analysed using the Grounded Theory method.
were validated and approved by the interviewed parents.
The certainty of the diagnosis was central for parents' experiences. First, the emotional reaction of the parents is highly influenced by the diagnostic process. Second, parents needed possibilities for taking action, and third they found difficulty in coping with an uncertain future. These three themes all related to the meaning that parents ascribed to the stating of a diagnosis. Parents' needs in relation to communication were identified as equality in co-operation with doctors, an empathic professional approach, and the child being seen with possibilities despite his or her disabilities.
Parents' process of realization was related to the diagnostic process, and information and communication should be individualized accordingly. Parents wanted to co-operate and they needed possibilities for active coping with their situation.