Genetic testing and counseling for the unexplained epilepsies: An evidence‐based practice guideline of the National Society of Genetic Counselors

Breaking barriers: fostering equitable access to pediatric genomics through innovative care models and technologies

The integration of genomic medicine into pediatric clinical practice is a critical need that remains largely unmet, especially in socioeconomically challenged and rural areas where healthcare disparities are most pronounced. This review seeks to summarize the barriers responsible for delayed diagnosis and treatment, and examines diverse care models, technological innovations, and strategies for dissemination and implementation aimed at addressing the evolving genomic needs of pediatric populations. Through a comprehensive review of the literature, we explore proposed methodologies to bridge this gap in pediatric healthcare, with a specific emphasis on understanding and speeding implementation approaches and technologies to mitigate disparities in underserved populations, including rural and marginalized communities. There are both external and internal factors to consider in demographic and social determinants when evaluating patient access. To address these barriers, potential solutions include telegenetic services, alternative care delivery models, pediatric subspecialist expansion, and non-genetic provider education. By improving access to pediatric genomic services, therapeutic interventions will also be more available to all pediatric patients. IMPACT STATEMENT: Genomic testing has clinical utility in pediatric populations but access for people from diverse demographic and social-economic groups is problematic. Understanding barriers responsible for delayed genetic diagnosis and treatment in pediatric populations will improve reach, adoption, implementation, and maintenance of genomic medicine in pediatric healthcare context. Innovative care models, adaptation of appropriate technologies, and strategies aimed at addressing pediatric genomic needs are needed.

The significance of interictal electroencephalogram analysis based on the grand total electroencephalogram score in early assessment of cognitive impairment in epilepsy patients

PURPOSE

Epilepsy is a widespread neurological disorder that increases the risk of cognitive impairment (CI) or dementia. We aimed to assess the relationship between cognition and interictal electroencephalogram (EEG) in epilepsy patients, using the Grand Total EEG (GTE) score. Additionally, we investigated the GTE score's utility in the early detection of CI in these patients.

METHODS

Data from 93 patients diagnosed with unexplained epilepsy at the Affiliated Hospital of Yangzhou University were analyzed. EEG recordings and cognitive evaluations were performed. Patients were categorized into three groups based on their Montreal Cognitive Assessment (MoCA) scores: normal cognitive (NC) group, mild cognitive impairment (MCI) group, and dementia group. The study included analysis of correlations between cognitive test results and clinical characteristics. Additionally, the influence of GTE scores and subscores on cognition was examined. Statistical analyses included one-way analysis of variance (ANOVA), Kruskal-Wallis H-test, Mann-Whitney U-test, Chi-square test, Spearman rank correlation analysis, and multiple linear regression.

RESULTS

(1) There was a significant negative correlation between cognitive test scores and GTE scores. Strong negative correlations were found between cognition (MoCA) and the GTE score (ρ = -0.754, P < 0.001), as well as for the subscores "Diffuse Slow Activity" (ρ = -0.712, P < 0.001), "Frequency of Rhythmic Background Activity" (ρ = -0.490, P < 0.001), and "Paroxysmal Activity" (ρ = -0.565, P < 0.001). (2) Multiple linear regression analysis identified the GTE score, "Diffuse Slow Activity", "Paroxysmal Activity", age, and education as significant predictors of cognitive decline. (3) At a threshold of 4.5, the GTE score effectively differentiated between individuals with and without CI, demonstrating a sensitivity of 73.8 % and a specificity of 93.7 %.

CONCLUSION

The GTE score provides clinically valuable information for the early detection of CI in patients with epilepsy. As CI worsens in epilepsy patients, the GTE score, Diffuse Slow Activity, Frequency of Rhythmic Background Activity, and Paroxysmal Activity increase. Healthcare providers should focus on managing not only seizures but also interictal EEG abnormalities to prevent or mitigate the risk of CI.

Diagnostic yields of genetic testing and related benefits in infantile epileptic spasms syndrome: A systematic review and meta-analysis

BACKGROUND

Diagnostic yields for infantile epileptic spasms syndrome (IESS) are notably heterogeneous across different testing modalities and studies. To investigate the proportion of individuals with IESS harboring causative/pathogenic genetic variants identified using whole-exome sequencing (WES), multi-gene panels (MGPs), and chromosomal microarray (CMA), thereby providing evidence to inform guidelines for genetic testing strategies.

METHODS

The study team searched PubMed, Embase, and Cochrane Central Register of Controlled Trials between January 2012- October2023. Data were extracted and synthesized by two investigators following the preferred reporting items for systematic reviews and meta-analyses guideline. The primary outcome was the pooled diagnostic rate of individual WES, MGPs, and CMA across studies. Subgroup analyses were performed based on the inclusion of cases with tuberous sclerosis complex and the number of genes included on MGPs.

RESULTS

Our study included 30 studies, involving 2 738 participants. The diagnostic rates in IESS for WES (13 studies, n = 799), MGPs (13 studies, n = 1 117), and CMA (13 studies, n = 629) were 26 % (95 % CI = 21 %-31 %), 20 % (95 % CI = 15 %-27 %), and 14 % (95 % CI = 11 %-16 %), respectively. WES and MGPs showed comparable diagnostic yields (P = 0.34). Our results indicated that 61.6 % of individuals with genetic IESS may potentially benefit from genetic diagnosis in terms of clinical management.

CONCLUSIONS

Our results showed that WES and MGPs exhibited comparable genetic diagnostic yields. Therefore, either method could be equally recommended as a first-tier testing approach for IESS cases with suspected genetic or unknown etiologies, especially considering the potential clinical benefits derived from genetic diagnosis.

Inherited metabolic epilepsies-established diseases, new approaches

Inherited metabolic epilepsies (IMEs) represent the inherited metabolic disorders (IMDs) in which epilepsy is a prevailing component, often determining other neurodevelopmental outcomes associated with the disorder. The different metabolic pathways affected by individual IMEs are the basis of their rarity and heterogeneity. These characteristics make it particularly challenging to establish their targeted therapies, and many of the IMEs are treated nowadays only symptomatically and supportively. However, owing to immense molecular and genetic progress in the last decades, important features of their pathomechanisms have been elucidated. This has led to advancements in the development of novel diagnostic approaches and specific therapies for a considerable number of these unique disorders. This review provides an overview of the broad approach to the diagnosis and management of IMEs, along with their eminent and new individual treatment options, ranging from dietary therapies and vitamins to enzyme and gene replacement therapies. PLAIN LANGUAGE SUMMARY: Inherited metabolic disorders (IMDs) in which epilepsy is a main symptom are considered inherited metabolic epilepsies (IMEs). It is challenging to develop targeted therapies for IMEs since they are rare and individually different in characteristics. Therefore, many of the IMEs are currently treated only symptomatically. However, scientific progress in the last decades led to the creation of specific treatments for many of these unique disorders. This review provides an overview of the approach to the diagnosis and management of IMEs, including the available newer therapeutic modalities.

Therapeutic implications of etiology-specific diagnosis of early-onset developmental and epileptic encephalopathies (EO-DEEs): A nationwide Turkish cohort study

OBJECTIVE

To evaluate the etiology-specific diagnosis of early-onset developmental epileptic encephalopathies (EO-DEEs) in a nationwide Turkish cohort to determine the implications for therapeutic management.

METHODS

The cohort comprised 1450 patients who underwent EO-DEE. The utility of genetic testing was assessed with respect to the initial phases of next generation sequencing (NGS) (2005-2013) and the current NGS era (2014-2022). A predefined four-stepwise diagnostic model was evaluated using cost-effectiveness analysis. The diagnostic and potential therapeutic yields of the genetic tests were subsequently determined.

RESULTS

Gene-related EO-DEEs were identified in 48.3 % (n = 701) of the cohort: non-structural genetic (62.6 %), metabolic genetic (15.1 %), and structural genetic (14.1 %). The most common nonstructural genetic variants were SCN1A (n = 132, 18.8 %), CDKL5 (n = 30, 4.2 %), STXBP1 (n = 21, 2.9 %), KCNQ2 (n = 21, 2.9 %), and PCDH19 (n = 17, 2.4 %). The rate of ultra-rare variants (< 0.5 %) was higher in the NGS era (52 %) than that in the initial phase (36 %). The potential therapeutic yields with precision therapy and antiseizure drug modification were defined in 34.5 % and 56.2 % in genetic-EO-DEEs, respectively. The diagnostic model provided an etiology-specific diagnosis at a rate of 78.7 %: structural (nongenetic) (31.4 %), genetic (38.5 %), metabolic (6.1 %), and immune-infectious (2.8 %). Based on a cost-effectiveness analysis, the presented diagnostic model indicated the early implementation of whole-exome sequencing for EO-DEEs.

SIGNIFICANCE

In the present cohort, the higher rate (48.3 %) of gene-related EO-DEE diagnoses in the NGS era provides a potential therapeutic management plan for more patients.

A Retrospective Review of Reclassification of Variants of Uncertain Significance in a Pediatric Epilepsy Cohort Undergoing Genetic Panel Testing

BACKGROUND

The interpretation and communication of variant of uncertain significance (VUS) genetic results often present a challenge in clinical practice. VUSs can be reclassified over time into benign/likely benign (B/LB) or pathogenic/likely pathogenic (P/LP) based on the availability of updated data. We evaluate the frequency of VUS reclassification in our tertiary care epilepsy cohort undergoing epilepsy genetic panel (EGP) testing.

METHODS

Patients with established diagnoses of epilepsy (neonates to 18 years of age) who underwent EGP testing between 2017 and 2022 from a single commercial laboratory were evaluated. Patients who had any variant reclassified from their initial EGP report were included. Duration between reclassification of VUSs and types of reclassifications were compared between developmental and epileptic encephalopathy (DEE) versus non-DEE phenotypes.

RESULTS

Over the five years, 1025 probands were tested using EGP. Eighty-five probands (8%) had at least one genetic variant reclassified. A total of 252 initial VUSs were reported in the 85 probands, of which 113 (45%) VUSs were reclassified. Of 113 reclassification events, 21 (19%) were upgraded to P/LP and 92 (81%) were reclassified to B/LB. The median (interquartile range) duration between variant reinterpretations in the cohort was 12 (14.5) months. There were no significant differences in the duration between reclassification and the likelihood of reclassification of VUSs to B/LB or P/LP between the two groups (DEE versus non-DEE).

CONCLUSIONS

VUS reclassification over time can lead to clinically significant variant reinterpretation in patients with unknown genetic diagnoses. Periodic genomic test reinterpretation, preferably yearly, is recommended in routine clinical practice.

Genome Sequencing After Exome Sequencing in Pediatric Epilepsy

This cohort study examined the yield and use of genome sequencing after nondiagnostic exome sequencing for pediatric patients with unexplained epilepsy between August 2018 and May 2023.

DHDDS-related epilepsy with hippocampal atrophy: a case report

Developmental delay and seizures with or without movement abnormalities (DEDSM) is a neurodevelopmental phenotype associated with monoallelic mutations in the DHDDS gene. We report a novel case of DEDSM linked to a DHDDS variant (c.614G > A, p.Arg205Gln) in a 45-year-old Brazilian patient presenting with refractory epilepsy, ataxia, dystonia, parkinsonism, and global developmental delay. This is the first case to associate a DHDDS variant with hippocampal atrophy on neuroimaging. After adjustments in anticonvulsant therapy, seizure control was achieved, and the patient-who was previously unable to walk due to frequent falls attributed to myoclonic jerks-showed significant improvement in gait and mobility.

The "genetic test request": A genomic stewardship intervention for inpatient exome and genome orders at a tertiary pediatric hospital

PURPOSE

Exome sequencing (ES) and genome sequencing (GS) are useful tests to diagnose rare diseases in pediatric patients in critical care settings. Genomic test stewardship can increase the appropriate use of these tests leading to improved diagnostics and cost savings.

METHODS

A mandatory review of ES and GS orders for admitted patients was implemented in March 2023. Outcomes of the reviews, cost analysis, and subsequent test results through February 2024 were analyzed with descriptive statistics.

RESULTS

There were 444 genetic test request orders placed for 412 unique patients. Of these, 81 (18.2%) were redirected and 57 (12.8%) required modification after approval, leading to an overall cost savings of $345,821.00 or $778.88 per order. The combined diagnostic rate was 28.2% in this patient population.

CONCLUSION

Stewardship of ES/GS orders for pediatric inpatients is an effective tool to improve the appropriate usage of these genomic tests. Additional collaboration with stakeholders and expansion of genomic stewardship initiatives may shorten the diagnostic odyssey for critically ill pediatric patients and result in cost savings.

Assessing and attending to psychosocial concerns in genetic counseling: Proposing the BATHE method

The process of identifying and responding to patients' social, emotional, and psychological concerns is a required skill for training and practicing genetic counselors. Patients' health outcomes are improved when genetic counselors attend to these "psychosocial" concerns. Still, the process of eliciting, assessing, and attending to patients' psychosocial concerns in the genetic counseling setting is not well defined in the literature nor is it performed consistently. Tools that do exist are often questionnaire-based, designed for research use, or occur outside of a genetic counseling appointment. Here we describe the complexities of defining "psychosocial assessment" in genetic counseling, its impact on patient outcomes, and summarize existing tools for psychosocial assessment. We identify a need for evidenced-based, verbally-administered psychosocial assessment tools in genetic counseling and explore the value of adapting an existing tool from primary care (the BATHE method) to genetic counseling. The BATHE method is a semi-structured psychosocial assessment tool that can be performed quickly within a patient appointment to gather context, emotional impact, the patient's primary concern, and coping strategies. Through our professional experiences we believe it is a beneficial psychosocial assessment tool as perceived by both patients and genetic counselors. Further work is needed to determine if the BATHE method could fill a gap in how genetic counselors conduct a psychosocial assessment.

Predicting Pediatric Genetic Epilepsy Through Electronic Medical Records: A Data-Driven Biomarker Discovery Approach

Clinical Signatures of Genetic Epilepsies Precede Diagnosis in Electronic Medical Records of 32  000 Individuals Galer PD, Parthasarathy S, Xian J, McKee JL, Ruggiero SM, Ganesan S, Kaufman MC, Cohen SR, Haag S, Chen C, Ojemann WKS, Kim D, Wilmarth O, Vaidiswaran P, Sederman C, Ellis CA, Gonzalez AK, Boßelmann CM, Lal D, Sederman R, Lewis-Smith D, Litt B, Helbig I. Genet Med. 2024101211. doi:10.1016/j.gim.2024.101211. PMID: 39011766 Purpose: An early genetic diagnosis can guide the time-sensitive treatment of individuals with genetic epilepsies. However, most genetic diagnoses occur long after disease onset. We aimed to identify early clinical features suggestive of genetic diagnoses in individuals with epilepsy through large-scale analysis of full-text electronic medical records (EMRs). Methods: We extracted 89 million time-stamped standardized clinical annotations using Natural Language Processing from 4,572,783 clinical notes from 32 112 individuals with childhood epilepsy, including 1925 individuals with known or presumed genetic epilepsies. We applied these features to train random forest models to predict SCN1A-related disorders and any genetic diagnosis. Results: We identified 47 774 age-dependent associations of clinical features with genetic etiologies a median of 3.6 years prior to molecular diagnosis. Across all 710 genetic etiologies identified in our cohort, neurodevelopmental differences between 6 and 9 months increased the likelihood of a later molecular diagnosis fivefold (P  < .0001, 95% CI = 3.55-7.42). A later diagnosis of SCN1A-related disorders (AUC = 0.91) or an overall positive genetic diagnosis (AUC = 0.82) could be reliably predicted using random forest models. Conclusion: Clinical features predictive of genetic epilepsies precede molecular diagnoses by up to several years in conditions with known precision treatments. An earlier diagnosis facilitated by automated EMR analysis has the potential for earlier targeted therapeutic strategies in the genetic epilepsies.

WONOEP appraisal: Genetic insights into early onset epilepsies

Early onset epilepsies occur in newborns and infants, and to date, genetic aberrations and variants have been identified in approximately one quarter of all patients. With technological sequencing advances and ongoing research, the genetic diagnostic yield for specific seizure disorders and epilepsies is expected to increase. Genetic variants associated with epilepsy include chromosomal abnormalities and rearrangements of various sizes as well as single gene variants. Among these variants, a distinction can be made between germline and somatic, with the latter being increasingly identified in epilepsies with focal cortical malformations in recent years. The identification of the underlying genetic mechanisms of epilepsy syndromes not only revolutionizes the diagnostic schemes but also leads to a better understanding of the diseases and their interrelationships, ultimately providing new opportunities for therapeutic targeting. At the XVI Workshop on Neurobiology of Epilepsy (WONOEP 2022, Talloires, France, July 2022), various etiologies, research models, and mechanisms of genetic early onset epilepsies were presented and discussed.

Clinical trials for Lennox-Gastaut syndrome: Challenges and priorities

OBJECTIVE

Lennox-Gastaut syndrome (LGS) is a severe, childhood-onset epilepsy that is typically refractory to treatment. We surveyed the current landscape of LGS treatment, aiming to identify challenges to the development of efficacious therapies, and to articulate corresponding priorities toward clinical trials that improve outcomes.

METHODS

The LGS Special Interest Group of the Pediatric Epilepsy Research Consortium integrated evidence from the literature and expert opinion, into a narrative review.

RESULTS

We provide an overview of approved and emerging medical, dietary, surgical and neuromodulation approaches for LGS. We note that quality of care could be improved by standardizing LGS treatment based on expert consensus and empirical data. Whereas LGS natural history is incompletely understood, prospective studies and use of large retrospective datasets to understand LGS across the lifespan would enable clinical trials that address these dynamics. Recent discoveries related to LGS pathophysiology should enable development of disease-modifying therapies, which are currently lacking. Finally, clinical trials have focused chiefly on seizures involving "drops," but should incorporate additional patient-centered outcomes, using emerging measures adapted to people with LGS.

INTERPRETATION

Clinicians and researchers should enact these priorities, with the goal of patient-centered clinical trials that are tailored to LGS pathophysiology and natural history.

Clinical signatures of genetic epilepsies precede diagnosis in electronic medical records of 32,000 individuals

PURPOSE

An early genetic diagnosis can guide the time-sensitive treatment of individuals with genetic epilepsies. However, most genetic diagnoses occur long after disease onset. We aimed to identify early clinical features suggestive of genetic diagnoses in individuals with epilepsy through large-scale analysis of full-text electronic medical records.

METHODS

We extracted 89 million time-stamped standardized clinical annotations using Natural Language Processing from 4,572,783 clinical notes from 32,112 individuals with childhood epilepsy, including 1925 individuals with known or presumed genetic epilepsies. We applied these features to train random forest models to predict SCN1A-related disorders and any genetic diagnosis.

RESULTS

We identified 47,774 age-dependent associations of clinical features with genetic etiologies a median of 3.6 years before molecular diagnosis. Across all 710 genetic etiologies identified in our cohort, neurodevelopmental differences between 6 to 9 months increased the likelihood of a later molecular diagnosis 5-fold (P < .0001, 95% CI = 3.55-7.42). A later diagnosis of SCN1A-related disorders (area under the curve [AUC] = 0.91) or an overall positive genetic diagnosis (AUC = 0.82) could be reliably predicted using random forest models.

CONCLUSION

Clinical features predictive of genetic epilepsies precede molecular diagnoses by up to several years in conditions with known precision treatments. An earlier diagnosis facilitated by automated electronic medical records analysis has the potential for earlier targeted therapeutic strategies in the genetic epilepsies.

Survey of the Landscape of Society Practice Guidelines for Genetic Testing of Neurodevelopmental Disorders

Genetic testing of patients with neurodevelopmental disabilities (NDDs) is critical for diagnosis, medical management, and access to precision therapies. Because genetic testing approaches evolve rapidly, professional society practice guidelines serve an essential role in guiding clinical care; however, several challenges exist regarding the creation and equitable implementation of these guidelines. In this scoping review, we assessed the current state of United States professional societies' guidelines pertaining to genetic testing for unexplained global developmental delay, intellectual disability, autism spectrum disorder, and cerebral palsy. We describe several identified shortcomings and argue the need for a unified, frequently updated, and easily-accessible cross-specialty society guideline. ANN NEUROL 2024;96:900-913.

CIC-Related Neurodevelopmental Disorder: A Review of the Literature and an Expansion of Genotype and Phenotype

BACKGROUND

Genetic testing for neurodevelopmental disorders is now considered the standard of care for unexplained epilepsy as well as autism spectrum disorders, intellectual disability, and developmental delays with as many as 50% of individuals identified as having an underlying genetic etiology. Capicua (CIC) is a transcriptional repressor and is widely expressed among human brain tissue. Patients in the literature with pathogenic variants in CIC present with a broad spectrum of phenotypic abnormalities. Common features include epilepsy, developmental delay, intellectual disability, autism spectrum disorder, and MRI abnormalities amongst other neurodevelopmental symptoms. Variant type, age of onset, sex, and severity of manifestation also differ amongst probands. However, the full genotypic and phenotypic spectrum of CIC-related neurodevelopmental disorder has not been elucidated.

METHODS

Here we review patients reported in the literature with CIC variants and present two additional patients representing a novel genotype and phenotype.

RESULTS

Whole exome sequencing (WES) in this proband identified a novel paternally inherited likely pathogenic variant in CIC c.1526del p.(Pro509Hisfs*14). Both proband and father present with isolated epilepsy without other significant neurodevelopmental disorders. A review of the previous literature identified 20 individuals harboring CIC variants; the majority of these individuals present with a combination of neurodevelopmental features. Sixteen distinct variants were identified amongst these 20 patients.

CONCLUSIONS

This family represents an expansion of the genotypic and phenotypic spectrum of CIC-related neurodevelopmental disorder. This information may lead to clinically actionable management changes for future patients identified with CIC variants considering standard anti-epileptic medication-weaning protocols.

Associations Between Testing and Treatment Pathways in a Case of Pediatric Nonlesional Epilepsy: A Census Survey of NAEC Center Directors

OBJECTIVE

Epilepsy surgery is vital in managing of children with drug-resistant epilepsy. Noninvasive and invasive testing modalities allow for evaluation and treatment of children with drug-resistant epilepsy. Evidence-based algorithms for this process do not exist. This study examines expert response to a vignette of pediatric nonlesional epilepsy to assess associations in evaluation and treatment choices.

METHODS

We analyzed annual report data and an epilepsy practice survey reported in 2020 from 135 pediatric epilepsy center directors in the United States. Characteristics of centers along with noninvasive and invasive testing and surgical treatment strategies were collected. Multivariable logistic regression modeling was performed.

RESULTS

The response rate was 100% with 135 responses included in the analyses. Most used noninvasive testing modalities included Neuropsychology evaluation (90%), interictal brain fluorodeoxyglucose-positron emission tomography (85%), and functional magnetic resonance imaging (MRI) (72%) with nearly half obtaining genetic testing. Choosing functional MRI was associated with stereo electroencephalography (EEG) (P = .025) and selecting Wada with subdural grid/strips (P = .038). Directors from pediatric-only centers were more likely to choose stereo EEG as opposed to combined centers (P = .042). Laser interstitial thermal therapy was almost 7 times as likely to be chosen as a treatment modality compared with open resection in dedicated pediatric centers (OR 6.96, P = .002).

SIGNIFICANCE

In a vignette of nonlesional childhood drug-resistant epilepsy, epilepsy center directors' patterns of noninvasive testing, invasive testing, and treatment were examined. Management choices were associated with pediatric versus combined pediatric/adult center characteristics. Expert opinions demonstrated equipoise in evaluation and management of children with drug-resistant epilepsy and the need for evidence-based management strategies.

Exome Sequencing of Consanguineous Pashtun Families With Familial Epilepsy Reveals Causative and Candidate Variants in TSEN54, MOCS2, and OPHN1

Next-generation sequencing is advancing in low- and middle-income countries, but accessibility remains limited. In Pakistan, many members of the Pashtun population practice familial marriage and maintain distinct socio-cultural traditions, isolating them from other ethnic groups. As a result, they may harbor genetic variants that could unveil new gene-disease associations. To investigate the genetic basis of epilepsy in the Pashtun community we recently established a collaboration between Bannu University and the University of Tuebingen. Here we report our first results of exome sequencing of four families with presumed monogenetic epilepsy and Mendelian inheritance pattern. In Family #201, we identified distinct disease-causing variants. One had a homozygous pathogenic missense variant in TSEN54 (c.919G > T, p.(Ala307Ser)), linked to Pontocerebellar Hypoplasia Type 2A. The second individual had a homozygous class IV missense variant in MOCS2 (c.226G > A, p.(Gly76Arg)) which is associated with Molybdenum cofactor deficiency. In family EP02, one affected individual carried a heterozygous class III variant in OPHN1 (c.1490G > A, p.(Arg497Gln)), related to syndromic X-linked intellectual disability with epilepsy. Our small study demonstrates the promise of next-generation sequencing in genetic epilepsies among the Pashtun population. Diagnostic next-generation sequencing should be established in Pakistan as soon as possible, and if not feasible, genetic research projects may pioneer this path.

Diagnostic evaluation of patients with epileptic spasms in the era of next-generation sequencing

OBJECTIVE

Epileptic spasms (ES) can be caused by a variety of etiologies. However, in almost half of cases, the etiology is unidentified. With the advent of next-generation sequencing (NGS), the recognition of genetic etiologies has increased.

METHODS

We retrospectively reviewed the medical records of patients with ES who were evaluated in the comprehensive epilepsy program at King Fahad Specialist Hospital Dammam between 2009 and 2022.

RESULTS

Our data show that in 57.7% of patients with ES, the etiology was unidentified after a standard clinical evaluation and neuroimaging. Of these patients, n = 25 (35.2%) received a genetic diagnosis after some form of genetic testing, and 3.1% of patients from specialized metabolic work indicated the need for genetic testing to confirm the diagnosis. Karyotyping led to a diagnosis in 3.6% of patients, and chromosomal microarray led to a diagnosis in 7.1%. An NGS epilepsy gene panel (EP) was done for 45 patients, leading to a diagnosis in 24.4% (n = 11). Exome sequencing was done for 27 patients, including n = 14 with non-diagnostic panel testing; it led to a diagnosis in 37.3% (n = 10). Exome sequencing led to a diagnosis in 61.5% of patients without a previous panel test and in only two patients who had previously had a negative panel testing.

SIGNIFICANCE

In this article, we present the diagnostic evaluations of ES for a cohort of 123 patients and discuss the yield and priority of NGS for evaluating ES. Our findings suggest that exome sequencing has a higher diagnostic yield for determining the etiology of ES in patients for whom the etiology is still unclear after an appropriate clinical assessment and a brain MRI.

Developmental and epileptic encephalopathies

Developmental and epileptic encephalopathies, the most severe group of epilepsies, are characterized by seizures and frequent epileptiform activity associated with developmental slowing or regression. Onset typically occurs in infancy or childhood and includes many well-defined epilepsy syndromes. Patients have wide-ranging comorbidities including intellectual disability, psychiatric features, such as autism spectrum disorder and behavioural problems, movement and musculoskeletal disorders, gastrointestinal and sleep problems, together with an increased mortality rate. Problems change with age and patients require substantial support throughout life, placing a high psychosocial burden on parents, carers and the community. In many patients, the aetiology can be identified, and a genetic cause is found in >50% of patients using next-generation sequencing technologies. More than 900 genes have been identified as monogenic causes of developmental and epileptic encephalopathies and many cell components and processes have been implicated in their pathophysiology, including ion channels and transporters, synaptic proteins, cell signalling and metabolism and epigenetic regulation. Polygenic risk score analyses have shown that common variants also contribute to phenotypic variability. Holistic management, which encompasses antiseizure therapies and care for multimorbidities, is determined both by epilepsy syndrome and aetiology. Identification of the underlying aetiology enables the development of precision medicines to improve the long-term outcome of patients with these devastating diseases.

Where there is no genetic counselor: An online decision-aid supports the majority of parents' diagnostic genomic testing choices for their children

PURPOSE

We evaluated DECIDE, an online pretest decision-support tool for diagnostic genomic testing, in nongenetics specialty clinics where there are no genetic counselors (GCs).

METHODS

Families of children offered genomic testing were eligible to participate. Fifty-six parents/guardians completed DECIDE at home, at their convenience. DECIDE includes an integrated knowledge quiz and decisional conflict screen. Six months later, parents were offered follow-up questionnaires and interviews about their experiences.

RESULTS

Forty parents (71%) had sufficient knowledge and no decisional conflict surrounding their testing decision, but 6 of this group had residual questions. These 6, plus 16 with decisional conflict or insufficient knowledge, saw a GC. At follow-up, little-to-no decisional regret and few negative emotions were identified in any parents. Most chose testing and described their decision as easy, yet stressful, and described many motivations for sequencing. Parents appreciated the simple comprehensive information DECIDE provided and the ability to view it in a low-stress environment.

CONCLUSION

DECIDE provides adequate decision-support to enable most parents to make value-consistent choices about genetic testing for their child. Parents reported that DECIDE helped to clarify motivations for pursuing (or declining) testing. DECIDE is a timely, well-tested, and accessible tool in clinical settings without GCs.

Diagnostic and clinical utility of comprehensive multigene panel testing for patients with neuropathy

BACKGROUND AND AIMS

Prior to next-generation sequencing (NGS), the evaluation of a patient with neuropathy typically consisted of screening for acquired causes, followed by clinical genetic testing of PMP22, MFN2, GJB1, and MPZ in patients with a positive family history and symptom onset prior to age 50. In this study, we examined the clinical utility of NGS in a large cohort of patients analyzed in a commercial laboratory.

METHODS

A cohort of 6849 adult patients underwent clinician-ordered peripheral neuropathy multigene panel testing ranging from 66 to 111 genes that included NGS and intragenic deletion/duplication analysis.

RESULTS

A molecular diagnosis was identified for 8.4% of the cohort (n = 573/6849). Variants in PMP22, MFN2, GJB1, MPZ, and TTR accounted for 73.8% of molecular diagnoses. Results had potential clinical actionability for 398 (69.5%) patients. Our results suggest that 225/573 (39.3%) of molecular diagnoses and 113/398 (28.4%) of clinical interventions would have been missed if the testing approach had been restricted to older guidelines.

INTERPRETATION

Our results highlight the need for expanded genetic testing guidelines that account for the increased number of genes associated with hereditary neuropathy, address the overlap of acquired and hereditary neuropathy, and provide broader access to genetic diagnosis for patients.

Utility of Genome Sequencing After Nondiagnostic Exome Sequencing in Unexplained Pediatric Epilepsy

Importance

Epilepsy is the most common neurological disorder of childhood. Identifying genetic diagnoses underlying epilepsy is critical to developing effective therapies and improving outcomes. Most children with non-acquired (unexplained) epilepsy remain genetically unsolved, and the utility of genome sequencing after nondiagnostic exome sequencing is unknown.

Objective

To determine the diagnostic (primary) and clinical (secondary) utility of genome sequencing after nondiagnostic exome sequencing in individuals with unexplained pediatric epilepsy.

Design

This cohort study performed genome sequencing and comprehensive analyses for 125 participants and available biological parents enrolled from August 2018 to May 2023, with data analysis through April 2024 and clinical return of diagnostic and likely diagnostic genetic findings. Clinical utility was evaluated.

Setting

Pediatric referral center.

Participants

Participants with unexplained pediatric epilepsy and previous nondiagnostic exome sequencing; biological parents when available.

Exposures

Short-read genome sequencing and analysis.

Main Outcomes and Measures

Primary outcome measures were the diagnostic yield of genome sequencing, defined as the percentage of participants receiving a diagnostic or likely diagnostic genetic finding, and the unique diagnostic yield of genome sequencing, defined as the percentage of participants receiving a diagnostic or likely diagnostic genetic finding that required genome sequencing. The secondary outcome measure was clinical utility of genome sequencing, defined as impact on evaluation, treatment, or prognosis for the participant or their family.

Results

125 participants (58 [46%] female) were enrolled with median age at seizure onset 3 [IQR 1.25, 8] years, including 44 (35%) with developmental and epileptic encephalopathies. The diagnostic yield of genome sequencing was 7.2% (9/125), with diagnostic genetic findings in five cases and likely diagnostic genetic findings in four cases. Among the solved cases, 7/9 (78%) required genome sequencing for variant detection (small copy number variant, three noncoding variants, and three difficult to sequence small coding variants), for a unique diagnostic yield of genome sequencing of 5.6% (7/125). Clinical utility was documented for 4/9 solved cases (44%).

Conclusions and Relevance

These findings suggest that genome sequencing can have diagnostic and clinical utility after nondiagnostic exome sequencing and should be considered for patients with unexplained pediatric epilepsy.

Genetic testing for unexplained epilepsy: A review of diagnostic approach, benefits, and referral algorithm

In the last several decades, advances in genetic testing have transformed the diagnostic and therapeutic approach to pediatric epilepsy. However, the interpretation of these genetic tests often requires expert analysis and counseling. For this reason, as our molecular understanding of the linkages between abnormal cerebral physiology and genetics has grown, so too has the field of clinical epilepsy genetics. Here we explore recent advances in genetic testing, describe the benefits of genetic testing in epilepsy, and provide a practice guideline for testing and referrals to specialized epilepsy genetics centers, highlighting the Epilepsy NeuroGenetics Initiative (ENGIN) Clinic and the Center for Epilepsy and Neurodevelopmental Disorders (ENDD) at the Children's Hospital of Philadelphia as an illustration of such a specialized center.

Global modified Delphi consensus on diagnosis, phenotypes, and treatment of SCN8A-related epilepsy and/or neurodevelopmental disorders

OBJECTIVE

We aimed to develop consensus for diagnosis/management of SCN8A-related disorders. Utilizing a modified Delphi process, a global cohort of experienced clinicians and caregivers provided input on diagnosis, phenotypes, treatment, and management of SCN8A-related disorders.

METHODS

A Core Panel (13 clinicians, one researcher, six caregivers), divided into three subgroups (diagnosis/phenotypes, treatment, comorbidities/prognosis), performed a literature review and developed questions for the modified Delphi process. Twenty-eight expert clinicians, one researcher, and 13 caregivers from 16 countries participated in the subsequent three survey rounds. We defined consensus as follows: strong consensus, ≥80% fully agree; moderate consensus, ≥80% fully/partially agree, <10% disagree; and modest consensus, 67%-79% fully/partially agree, <10% disagree.

RESULTS

Early diagnosis is important for long-term clinical outcomes in SCN8A-related disorders. There are five phenotypes: three with early seizure onset (severe developmental and epileptic encephalopathy [DEE], mild/moderate DEE, self-limited (familial) infantile epilepsy [SeL(F)IE]) and two with later/no seizure onset (neurodevelopmental delay with generalized epilepsy [NDDwGE], NDD without epilepsy [NDDwoE]). Caregivers represented six patients with severe DEE, five mild/moderate DEE, one NDDwGE, and one NDDwoE. Phenotypes vary by age at seizures/developmental delay onset, seizure type, electroencephalographic/magnetic resonance imaging findings, and first-line treatment. Gain of function (GOF) versus loss of function (LOF) is valuable for informing treatment. Sodium channel blockers are optimal first-line treatment for GOF, severe DEE, mild/moderate DEE, and SeL(F)IE; levetiracetam is relatively contraindicated in GOF patients. First-line treatment for NDDwGE is valproate, ethosuximide, or lamotrigine; sodium channel blockers are relatively contraindicated in LOF patients.

SIGNIFICANCE

This is the first-ever global consensus for the diagnosis and treatment of SCN8A-related disorders. This consensus will reduce knowledge gaps in disease recognition and inform preferred treatment across this heterogeneous disorder. Consensus of this type allows more clinicians to provide evidence-based care and empowers SCN8A families to advocate for their children.

The Utility of Genetic Testing in Infantile Epileptic Spasms Syndrome: A Step-Based Approach in the Next-Generation Sequencing Era

BACKGROUND

To evaluate the utility of genetic testing for etiology-specific diagnosis (ESD) in infantile epileptic spasms syndrome (IESS) with a step-based diagnostic approach in the next-generation sequencing (NGS) era.

METHODS

The study cohort consisted of 314 patients with IESS, followed by the Pediatric Neurology Division of Ege University Hospital between 2005 and 2021. The ESD was evaluated using a step-based approach: step I (clinical phenomenology), step II (neuroimaging), step III (metabolic screening), and step IV (genetic testing). The diagnostic utility of genetic testing was evaluated to compare the early-NGS period (2005 to 2013, n = 183) and the NGS era (2014 to 2021, n = 131).

RESULTS

An ESD was established in 221 of 314 (70.4%) infants with IESS: structural, 40.8%; genetic, 17.2%; metabolic, 8.3%; immune-infectious, 4.1%. The diagnostic yield of genetic testing increased from 8.9% to 41.7% in the cohort during the four follow-up periods. The rate of unknown etiology decreased from 34.9% to 22.1% during the follow-up periods. The genetic ESD was established as 27.4% with genetic testing in the NGS era. The genetic testing in the NGS era increased dramatically in subgroups with unknown and structural etiologies. The diagnostic yields of the epilepsy panels increased from 7.6% to 19.2%. However, the diagnostic yield of whole exome sequencing remained at similar levels during the early-NGS period at 54.5% and in the NGS era at 59%.

CONCLUSIONS

The more genetic ESD (27.4%) was defined for IESS in the NGS era with the implication of precision therapy (37.7%).

Genetic Testing in Pediatric Epilepsy: Tools, Tips, and Navigating the Traps

With the advent of high-throughput sequencing and computational methods, genetic testing has become an integral part of contemporary clinical practice, particularly in epilepsy. The toolbox for genetic testing has evolved from conventional chromosomal microarray and epilepsy gene panels to state-of-the-art sequencing techniques in the modern genomic era. Beyond its potential for therapeutic benefits through precision medicine, optimizing the choice of antiseizure medications, or exploring nonpharmacological therapeutic modalities, genetic testing carries substantial diagnostic, prognostic, and personal implications. Developmental and epileptic encephalopathies, the coexistence of neurodevelopmental comorbidities, early age of epilepsy onset, unexplained drug-refractory epilepsy, and positive family history have demonstrated the highest likelihood of yielding positive genetic test results. Given the diagnostic efficacy across different testing modalities, reducing costs of next-generation sequencing tests, and genetic diversity of epilepsies, exome sequencing or genome sequencing, where feasible and available, have been recommended as the first-tier test. Comprehensive clinical phenotyping at the outset, corroborative evidence from radiology and electrophysiology-based investigations, reverse phenotyping, and periodic reanalysis are some of the valuable strategies when faced with inconclusive test results. In this narrative review, the authors aim to simplify the approach to genetic testing in epilepsy by guiding on the selection of appropriate testing tools in the indicated clinical scenarios, addressing crucial aspects during pre- and post-test counseling sessions, adeptly navigating the traps posed by uncertain or negative genetic variants, and paving the way forward to the emerging testing modalities beyond DNA sequencing.

Zebrafish models of candidate human epilepsy-associated genes provide evidence of hyperexcitability

Hundreds of novel candidate human epilepsy-associated genes have been identified thanks to advancements in next-generation sequencing and large genome-wide association studies, but establishing genetic etiology requires functional validation. We generated a list of >2,200 candidate epilepsy-associated genes, of which 48 were developed into stable loss-of-function (LOF) zebrafish models. Of those 48, evidence of seizure-like behavior was present in 5 (arfgef1, kcnd2, kcnv1, ubr5, and wnt8b). Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally, arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further, RNA sequencing (RNA-seq) revealed convergent transcriptional abnormalities between mutant lines, consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1, KCND2, and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.

Out of Sight, Not Yet Out of Reach: Surgical Outcomes in MRI-Negative and Pathology-Negative Epilepsy Patients

Outcome of Epilepsy Surgery in MRI-Negative Patients Without Histopathologic Abnormalities in the Resected Tissue Sanders MW, Van der Wolf I, Jansen FE, Aronica E, Helmstaedter C, Racz A, Surges R, Grote A, Becker AJ, Rheims S, Catenoix H, Duncan JS, De Tisi J, Jacques TS, Cross JH, Kalviainen R, Rauramaa T, Chassoux F, Devaux BC, Di Gennaro G, Esposito V, Bodi I, Honavar M, Bien CG, Cloppenborg T, Coras R, Hamer HM, Marusic P, Kalina A, Pieper T, Kudernatsch M, Hartlieb TS, Von Oertzen TJ, Aichholzer M, Dorfmuller G, Chipaux M, Noachtar S, Kaufmann E, Schulze-Bonhage A, Scheiwe CF, Özkara C, Grunwald T, Koenig K, Guerrini R, Barba C, Buccoliero AM, Giordano F, Rosenow F, Menzler K, Garbelli R, Deleo F, Krsek P, Straka B, Arzimanoglou AA, Toulouse J, Van Paesschen W, Theys T, Pimentel J, Loução De Amorim IM, Specchio N, De Palma L, Feucht M, Scholl T, Roessler K, Toledano Delgado R, Gil-Nagel A, Raicevic S, Ristic AJ, Schijns O, Beckervordersandforth J, San Antonio-Arce V, Rumia J, Blumcke I, Braun KP; as the European Epilepsy Brain Bank Consortium (EEBB). Neurology . 2024;102(4): e208007. doi:10.1212/WNL.0000000000208007 . PMID: 38290094 Background and Objectives: Patients with presumed nonlesional focal epilepsy—based on either MRI or histopathologic findings—have a lower success rate of epilepsy surgery compared with lesional patients. In this study, we aimed to characterize a large group of patients with focal epilepsy who underwent epilepsy surgery despite a normal MRI and had no lesion on histopathology. Determinants of their postoperative seizure outcomes were further studied. Methods: We designed an observational multicenter cohort study of MRI-negative and histopathology-negative patients who were derived from the European Epilepsy Brain Bank and underwent epilepsy surgery between 2000 and 2012 in 34 epilepsy surgery centers within Europe. We collected data on clinical characteristics, presurgical assessment, including genetic testing, surgery characteristics, postoperative outcome, and treatment regimen. Results: Of the 217 included patients, 40% were seizure-free (Engel I) 2 years after surgery and one-third of patients remained seizure-free after 5 years. Temporal lobe surgery (adjusted odds ratio [AOR]: 2.62; 95% CI 1.19-5.76), shorter epilepsy duration (AOR for duration: 0.94; 95% CI 0.89-0.99), and completely normal histopathologic findings—versus nonspecific reactive gliosis—(AOR: 4.69; 95% CI 1.79-11.27) were significantly associated with favorable seizure outcome at 2 years after surgery. Of patients who underwent invasive monitoring, only 35% reached seizure freedom at 2 years. Patients with parietal lobe resections had lowest seizure freedom rates (12.5%). Among temporal lobe surgery patients, there was a trend toward favorable outcome if hippocampectomy was part of the resection strategy (OR: 2.94; 95% CI 0.98-8.80). Genetic testing was only sporadically performed. Discussion: This study shows that seizure freedom can be reached in 40% of nonlesional patients with both normal MRI and histopathology findings. In particular, nonlesional temporal lobe epilepsy should be regarded as a relatively favorable group, with almost half of patients achieving seizure freedom at 2 years after surgery-even more if the hippocampus is resected-compared with only 1 in 5 nonlesional patients who underwent extratemporal surgery. Patients with an electroclinically identified focus, who are nonlesional, will be a promising group for advanced molecular-genetic analysis of brain tissue specimens to identify new brain somatic epilepsy genes or epilepsy-associated molecular pathways.

Comparing the frequency of variants of uncertain significance (VUS) between ancestry groups in a paediatric epilepsy cohort

BACKGROUND

Studies indicate that variants of uncertain significance are more common in non-European populations due to lack of a diversity in population databases. This difference has not been explored in epilepsy, which is increasingly found to be genetic in paediatric populations, and has precision medicine applications. This study examines the differences in the frequency of uncertain next-generation sequencing (NGS) results among a paediatric epilepsy cohort between ancestral groups historically under-represented in biomedical research (UBR) and represented in biomedical research (RBR).

METHODS

A retrospective chart review of patients with epilepsy seen at Columbia University Irving Medical Center (CUIMC). One hundred seventy-eight cases met the following criteria: (1) visited any provider within the Pediatric Neurology Clinic at CUIMC, (2) had an ICD code indicating a diagnosis of epilepsy, (3) underwent NGS testing after March 2015 and (4) had self-reported ancestry that fit into a single dichotomous category of either historically represented or under-represented in biomedical research.

RESULTS

UBR cases had significantly higher rates of uncertain results when compared with RBR cases (79.2% UBR, 20.8% RBR; p value=0.002). This finding remained true after controlling for potential confounding factors, including sex, intellectual disability or developmental delay, epilepsy type, age of onset, number of genes tested and year of testing.

CONCLUSION

Our results add to the literature that individuals who are of ancestries historically under-represented in genetics research are more likely to receive uncertain genetic results than those of represented majority ancestral groups and establishes this finding in an epilepsy cohort.

Rapid Whole Genome Sequencing: It Is Feasible! When Can We Implement It?

Evaluation of the Feasibility, Diagnostic Yield, and Clinical Utility of Rapid Genome Sequencing in Infantile Epilepsy (Gene-STEPS): An International, Multicentre, Pilot Cohort Study D’Gama AM, Mulhern S, Sheidley BR, Boodhoo F, Buts S, Chandler NJ, Cobb J, Curtis M, Higginbotham EJ, Holland J, Khan T, Koh J, Liang NSY, McRae L, Nesbitt SE, Oby BT, Paternoster B, Patton A, Rose G, Scotchman E, Valentine R, Wiltrout KN; Gene-STEPS Study Group; IPCHiP Executive Committee; Hayeems RZ, Jain P, Lunke S, Marshall CR, Rockowitz S, Sebire NJ, Stark Z, White SM, Chitty LS, Cross JH, Scheffer IE, Chau V, Costain G, Poduri A, Howell KB, McTague A. Lancet Neurol. 2023;22(9):812-825. doi:10.1016/S1474-4422(23)00246-6 Background: Most neonatal and infantile-onset epilepsies have presumed genetic aetiologies, and early genetic diagnoses have the potential to inform clinical management and improve outcomes. We therefore aimed to determine the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in this population. Methods: We conducted an international, multicentre, cohort study (Gene-STEPS), which is a pilot study of the International Precision Child Health Partnership (IPCHiP). IPCHiP is a consortium of four paediatric centres with tertiary-level subspecialty services in Australia, Canada, the UK, and the USA. We recruited infants with new-onset epilepsy or complex febrile seizures from IPCHiP centres, who were younger than 12 months at seizure onset. We excluded infants with simple febrile seizures, acute provoked seizures, known acquired cause, or known genetic cause. Blood samples were collected from probands and available biological parents. Clinical data were collected from medical records, treating clinicians, and parents. Trio genome sequencing was done when both parents were available, and duo or singleton genome sequencing was done when one or neither parent was available. Site-specific protocols were used for DNA extraction and library preparation. Rapid genome sequencing and analysis was done at clinically accredited laboratories, and results were returned to families. We analysed summary statistics for cohort demographic and clinical characteristics and the timing, diagnostic yield, and clinical impact of rapid genome sequencing. Findings: Between Sept 1, 2021, and Aug 31, 2022, we enrolled 100 infants with new-onset epilepsy, of whom 41 (41%) were girls and 59 (59%) were boys. Median age of seizure onset was 128 days (IQR 46-192). For 43 (43% [binomial distribution 95% CI 33-53]) of 100 infants, we identified genetic diagnoses, with a median time from seizure onset to rapid genome sequencing result of 37 days (IQR 25-59). Genetic diagnosis was associated with neonatal seizure onset versus infantile seizure onset (14 [74%] of 19 vs 29 [36%] of 81; p = 0.0027), referral setting (12 [71%] of 17 for intensive care, 19 [44%] of 43 non-intensive care inpatient, and 12 [28%] of 40 outpatient; p = 0.0178), and epilepsy syndrome (13 [87%] of 15 for self-limited epilepsies, 18 [35%] of 51 for developmental and epileptic encephalopathies, 12 [35%] of 34 for other syndromes; p = 0.001). Rapid genome sequencing revealed genetic heterogeneity, with 34 unique genes or genomic regions implicated. Genetic diagnoses had immediate clinical utility, informing treatment (24 [56%] of 43), additional evaluation (28 [65%]), prognosis (37 [86%]), and recurrence risk counselling (all cases). Interpretation: Our findings support the feasibility of implementation of rapid genome sequencing in the clinical care of infants with new-onset epilepsy. Longitudinal follow-up is needed to further assess the role of rapid genetic diagnosis in improving clinical, quality-of-life, and economic outcomes.

CDKL5 deficiency disorder and other infantile-onset genetic epilepsies

AIM

To differentiate phenotypic features of individuals with CDKL5 deficiency disorder (CDD) from those of individuals with other infantile-onset epilepsies.

METHOD

We performed a retrospective cohort study and ascertained individuals with CDD and comparison individuals with infantile-onset epilepsy who had epilepsy gene panel testing. We reviewed records, updated variant classifications, and compared phenotypic features. Wilcoxon rank-sum tests and χ2 or Fisher's exact tests were performed for between-cohort comparisons.

RESULTS

We identified 137 individuals with CDD (110 females, 80.3%; median age at last follow-up 3 year 11 months) and 313 individuals with infantile-onset epilepsies (156 females, 49.8%; median age at last follow-up 5 years 2 months; 35% with genetic diagnosis). Features reported significantly more frequently in the CDD group than in the comparison cohort included developmental and epileptic encephalopathy (81% vs 66%), treatment-resistant epilepsy (95% vs 71%), sequential seizures (46% vs 6%), epileptic spasms (66% vs 42%, with hypsarrhythmia in 30% vs 48%), regression (52% vs 29%), evolution to Lennox-Gastaut syndrome (23% vs 5%), diffuse hypotonia (72% vs 36%), stereotypies (69% vs 11%), paroxysmal movement disorders (29% vs 17%), cerebral visual impairment (94% vs 28%), and failure to thrive (38% vs 22%).

INTERPRETATION

CDD, compared with other suspected or confirmed genetic epilepsies presenting in the first year of life, is more often characterized by a combination of treatment-resistant epilepsy, developmental and epileptic encephalopathy, sequential seizures, spasms without hypsarrhythmia, diffuse hypotonia, paroxysmal movement disorders, cerebral visual impairment, and failure to thrive. Defining core phenotypic characteristics will improve precision diagnosis and treatment.

Epilepsy panel testing criteria: A clinical assessment

Epilepsy is a common, and often genetic, neurological disorder. Few guidelines exist to help medical providers or insurance companies decide when to order or cover epilepsy panels for patients with epilepsy. The most recent guidelines were published by NSGC after this study's data collection. Since 2017, the Genetic Testing Stewardship Program (GTSP) at UPMC Children's Hospital of Pittsburgh (CHP) has been utilizing a set of internally developed epilepsy panel (EP) testing criteria to facilitate appropriate EP ordering practices. The purpose of this study was to assess these testing criteria by determining their sensitivities and positive predictive values (PPV). Retrospective chart review of the electronic medical record (EMR) was performed for 1242 CHP Neurology patients that were evaluated for a primary diagnosis of epilepsy between 2016 and 2018. One hundred and nine patients had EPs at various testing laboratories. Of the patients that met criteria, 17 had diagnostic EPs and 54 had negative EPs. Criteria were organized into category groupings (C1-C4), and analyzed alone for C1, in pairs for C2, etc. The highest sensitivity and PPV results in each category grouping were: C1 (64.7%, 60%); C2, (88%, 30.3%); C3, (94.1%, 27.1%); C4, (94.1%, 25.4%). Family history was crucial to increasing sensitivity. Confidence intervals (CIs) narrowed as category grouping level increased, though this was not statistically significant due to the considerable CI overlap across category groupings. The PPV from C4 was applied to the untested population cohort and predicted 121 patients with unidentified positive EPs. This study presents data supporting the predictive capabilities of EP testing criteria and suggests the addition of a family history criterion. This study impacts public health by encouraging the adoption of evidence-driven insurance policies and by suggesting guidelines to ease EP ordering and coverage decisions, which could potentially improve patient access to EP testing.

Genetic Testing in Epilepsy: Improving Outcomes and Informing Gaps in Research

While the diagnosis of epilepsy relies on the presence of seizures, it encompasses a group of phenotypically and etiologically diverse disorders in which seizures may only be one of a constellation of symptoms. There are genetic, structural, and metabolic causes, but most epilepsy syndromes have some genetic predisposition. The importance of genetics in the diagnosis and management of epilepsy has been increasingly recognized over the past 2 decades. With increased access to testing tools and new recommendations that all patients with unexplained epilepsy get genetic testing, it is becoming part of routine clinical care. Increased testing has resulted in an explosion in the number of genes and genetic changes identified and it is changing our understanding of the mechanisms of epileptogenesis. Advances in both clinical genetics and scientific discovery are expanding our potential to impact patient care as well as creating dilemmas. This brief review will highlight where we are regarding our ability to obtain a genetic diagnosis, how diagnoses impact patient care, and the next likely frontiers in diagnosis and management.

"Hole" Exome Sequences: The Importance of Phenotyping to Fill the Gaps in Whole Exome Sequencing

BACKGROUND

Whole exome sequencing (WES) is commonly used for patients with nonspecific clinical features and conditions with genetic heterogeneity. However, a nondiagnostic exome does not exclude a genetic diagnosis, so history and physical examination is crucial to selecting appropriate genetic testing.

CASES

We report three patients with three recognizable phenotypes: a seven-year-old female with classic Rett syndrome; a 28-year-old male with neuropathy, ataxia, and retinitis pigmentosa; and a 16-year-old male with mosaic, segmental, paternal uniparental disomy 14 who had nondiagnostic WES.

CONCLUSIONS

Despite recognizable phenotypes they had diagnostic delays due to incorrect selection of genetic testing. This case series highlights the limitations of WES and reinforces the importance of utilizing patient history and physical examination to select initial testing. We will discuss appropriate testing for these patients and a consistent diagnostic algorithm that can be applied when approaching patients with unknown or uncertain clinical presentations.

Common genes and recurrent causative variants in 957 Asian patients with pediatric epilepsy

OBJECTIVE

We aimed to identify common genes and recurrent causative variants in a large group of Asian patients with different epilepsy syndromes and subgroups.

METHODS

Patients with unexplained pediatric-onset epilepsy were identified from the in-house Severance Neurodevelopmental Disorders and Epilepsy Database. All patients underwent either exome sequencing or multigene panels from January 2017 to December 2019, at Severance Children's Hospital in Korea. Clinical data were extracted from the medical records.

RESULTS

Of the 957 patients studied, 947 (99.0%) were Korean and 570 were male (59.6%). The median age at testing was 4.91 years (interquartile range, 1.53-9.39). The overall diagnostic yield was 32.4% (310/957). Clinical exome sequencing yielded a diagnostic rate of 36.9% (134/363), whereas the epilepsy panel yielded a diagnostic rate of 29.9% (170/569). Diagnostic yield differed across epilepsy syndromes. It was high in Dravet syndrome (87.2%, 41/47) and early infantile developmental epileptic encephalopathy (60.7%, 17/28), but low in West syndrome (21.8%, 34/156) and myoclonic-atonic epilepsy (4.8%, 1/21). The most frequently implicated genes were SCN1A (n = 49), STXBP1 (n = 15), SCN2A (n = 14), KCNQ2 (n = 13), CDKL5 (n = 11), CHD2 (n = 9), SLC2A1 (n = 9), PCDH19 (n = 8), MECP2 (n = 6), SCN8A (n = 6), and PRRT2 (n = 5). The recurrent genetic abnormalities included 15q11.2 deletion/duplication (n = 9), Xq28 duplication (n = 5), PRRT2 deletion (n = 4), MECP2 duplication (n = 3), SCN1A, c.2556+3A>T (n = 3), and 2q24.3 deletion (n = 3).

SIGNIFICANCE

Here we present the results of a large-scale study conducted in East Asia, where we identified several common genes and recurrent variants that varied depending on specific epilepsy syndromes. The overall genetic landscape of the Asian population aligns with findings from other populations of varying ethnicities.

Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review

Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.

Genetic Advancements in Infantile Epileptic Spasms Syndrome and Opportunities for Precision Medicine

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.

Early genetic testing in pediatric epilepsy: Diagnostic and cost implications

The identification of numerous genetically based epilepsies has resulted in the widespread use of genetic testing to inform epilepsy etiology. Our study aims to investigate whether a difference exists in the diagnostic evaluation and healthcare-related cost expenditures of pediatric patients with epilepsy of unknown etiology who receive a genetic diagnosis through multigene epilepsy panel (MEP) testing and comparing those who underwent early (EGT) versus late genetic testing (LGT). Testing was defined as early (less than 1 year), or late (more than 1 year), following clinical epilepsy diagnosis. A retrospective chart review of pediatric individuals (1-17 years) with epilepsy of unknown etiology who underwent multigene epilepsy panel (MEP) testing identified 28 of 226 (12%) individuals with a pathogenic epilepsy variant [EGT n = 8 (29%); LGT n = 20 (71%)]. The average time from clinical epilepsy diagnosis to genetic diagnosis was 0.25 years (EGT), compared with 7.1 years (LGT). The EGT cohort underwent fewer metabolic tests [EGT n = 0 (0%); LGT n = 16 (80%) (P < 0.01)] and invasive procedures [EGT n = 0 (0%); LGT n = 5 (25%) (P = 0.06)]. Clinical management changes implemented due to genetic diagnosis occurred in 10 (36%) patients [EGT n = 2 (25%); LGT n = 8 (40%) (P = 0.76)]. Early genetic testing with a MEP in pediatric patients with epilepsy of unknown etiology who receive a genetic diagnosis is associated with fewer non-diagnostic tests and invasive procedures and reduced estimated overall healthcare-related costs. PLAIN LANGUAGE SUMMARY: This study aims to investigate whether a difference exists in the diagnostic evaluation and cost expenditures of pediatric patients (1-17 years) with epilepsy of unknown cause who are ultimately diagnosed with a genetic cause of epilepsy through multigene epilepsy panel testing and comparing those who underwent early testing (less than 1 year) versus late testing (more than 1 year) after clinical epilepsy diagnosis. Of the 28 of 226 individuals with a confirmed genetic cause of epilepsy on multigene epilepsy panel testing, performing early testing was associated with fewer non-diagnostic tests, fewer invasive procedures and reduced estimated overall healthcare-related costs.

Genetic testing in adults with neurologic disorders: indications, approach, and clinical impacts

The role of genetic testing in neurologic clinical practice has increased dramatically in recent years, driven by research on genetic causes of neurologic disease and increased availability of genetic sequencing technology. Genetic testing is now indicated for adults with a wide range of common neurologic conditions. The potential clinical impacts of a genetic diagnosis are also rapidly expanding, with a growing list of gene-specific treatments and clinical trials, in addition to important implications for prognosis, surveillance, family planning, and diagnostic closure. The goals of this review are to provide practical guidance for clinicians about the role of genetics in their practice and to provide the neuroscience research community with a broad survey of current progress in this field. We aim to answer three questions for the neurologist in practice: Which of my patients need genetic testing? What testing should I order? And how will genetic testing help my patient? We focus on common neurologic disorders and presentations to the neurology clinic. For each condition, we review the most current guidelines and evidence regarding indications for genetic testing, expected diagnostic yield, and recommended testing approach. We also focus on clinical impacts of genetic diagnoses, highlighting a number of gene-specific therapies recently approved for clinical use, and a rapidly expanding landscape of gene-specific clinical trials, many using novel nucleotide-based therapeutic modalities like antisense oligonucleotides and gene transfer. We anticipate that more widespread use of genetic testing will help advance therapeutic development and improve the care, and outcomes, of patients with neurologic conditions.

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup

OBJECTIVE

Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space.

PROCESS

A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members.

CONCLUSIONS

Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of larger datasets is crucial to emulating the success AI is achieving in other domains. It is important that AI methods do not exacerbate existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical to effectively scale such technologies across institutions. With so much uncertainty, complexity and novelty in genomics and medicine, and with an evolving regulatory environment, the current focus should be on using these technologies in an interface with clinicians that emphasizes the value each brings to clinical decision-making.

Next-generation sequencing testing in children with epilepsy reveals novel clinical, diagnostic and therapeutic implications

Introduction: Epilepsy is one of the commonest diseases in children, characterized by extensive phenotypic and genetic heterogeneity. This study was conducted to determine the diagnostic utility and to identify novel clinical and therapeutic implications of genetic testing in pediatric patients with epilepsy. Methods: Large multigene panel and/or exome sequencing was performed in 127 unrelated Polish and Ukrainian patients with suspected monogenic epilepsy. Diagnostic yields were presented for five phenotypic subgroups, distinguished by seizure type, electroencephalographic abnormalities, anti-seizure treatment response, and neurodevelopmental deficits. Results: A definite molecular diagnosis was established in 46 out of 127 cases (36%). Alterations in six genes were detected in more than one patient: SCN1A, MECP2, KCNT1, KCNA2, PCDH19, SLC6A1, STXBP1, and TPP1, accounting for 48% of positive cases. 4/46 cases (8.7%) were mosaic for the variant. Although the highest rates of positive diagnoses were identified in children with developmental delay and generalized seizures (17/41, 41%) and in developmental end epileptic encephalopathies (16/40, 40%), a monogenic etiology was also frequently detected in patients with solely focal seizures (10/28, 36%). Molecular diagnosis directly influenced anti-seizure management in 15/46 cases. Conclusion: This study demonstrates the high diagnostic and therapeutic utility of large panel testing in childhood epilepsies irrespective of seizure types. Copy number variations and somatic mosaic variants are important disease-causing factors, pointing the need for comprehensive genetic testing in all unexplained cases. Pleiotropy is a common phenomenon contributing to the growing phenotypic complexity of single-gene epilepsies.

Epilepsy and Encephalopathy

BACKGROUND

Epilepsy encompasses more than the predisposition to unprovoked seizures. In children, epileptic activity during (ictal) and between (interictal) seizures has the potential to disrupt normal brain development. The term "epileptic encephalopathy (EE)" refers to the concept that such abnormal activity may contribute to cognitive and behavioral impairments beyond that expected from the underlying cause of the epileptic activity.

METHODS

In this review, we survey the concept of EE across a diverse selection of syndromes to illustrate its broad applicability in pediatric epilepsy. We review experimental evidence that provides mechanistic insights into how epileptic activity has the potential to impact normal brain processes and the development of neural networks. We then discuss opportunities to improve developmental outcomes in epilepsy now and in the future.

RESULTS

Epileptic activity in the brain poses a threat to normal physiology and brain development.

CONCLUSION

Until we have treatments that reliably target and effectively treat the underlying causes of epilepsy, a major goal of management is to prevent epileptic activity from worsening developmental outcomes.

Clinical and biochemical footprints of inherited metabolic diseases. XV. Epilepsies

We provide a comprehensive overview of inherited metabolic disorders (IMDs) in which epilepsy is a prominent manifestation. Our unique database search has identified 256 IMDs associated with various types of epilepsies, which we classified according to the classic pathophysiology-based classification of IMDs, and according to selected seizure-related factors (neonatal seizures, infantile spasms, myoclonic seizures, and characteristic EEG patterns) and treatability for the underlying metabolic defect. Our findings indicate that inherited metabolic epilepsies are more likely to present in the neonatal period, with infantile spasms or myoclonic seizures. Additionally, the ∼20% of treatable inherited metabolic epilepsies found by our search were mainly associated with the IMD groups of "cofactor and mineral metabolism" and "Intermediary nutrient metabolism." The information provided by this study, including a comprehensive list of IMDs with epilepsy stratified according to age of onset, and seizure type and characteristics, along with an overview of the key clinical features and proposed diagnostic and therapeutic approaches, may benefit any epileptologist and healthcare provider caring for individuals with metabolic conditions.

Intellectual Disability and Epilepsy: The High Incidence and the Risks of Status Epilepticus and Sudden Death Require Improved Therapies

Epidemiology of Developmental and Epileptic Encephalopathy and of Intellectual Disability and Epilepsy in Children Poke G, Stanley J, Scheffer IE, Sadleir LG. Neurology. 2023;100(13):e1363-e1375. doi:10.1212/WNL.0000000000206758 Background and Objectives: We aimed to determine the population-based cumulative incidence and prevalence of developmental and epileptic encephalopathies (DEEs) and intellectual disability and epilepsy (ID+E) in children. We analyzed the cumulative incidence of specific epilepsy syndromes. Methods: Children younger than 16 years with a DEE or ID+E were ascertained using EEG records from 2000 to 2016 in the Wellington region of New Zealand. Epilepsy syndromes were diagnosed on medical record and EEG review. Point prevalence and cumulative incidence for children with epilepsy and developmental impairment, DEE and ID+E were calculated. Cumulative incidence for each epilepsy syndrome was calculated. Results: The cohort comprised 235 children (58% male) with developmental impairment and epilepsy, including 152 (65%) with DEE and 83 (35%) with ID+E. The median age of seizure onset was 15.4 months (range day 1-15 years). The median follow-up from seizure onset was 7.9 years (range 0-18.2 years). Point prevalence for the broad group of children with epilepsy and developmental impairment was 175/100,000 children (95% CI 149-203; DEE 112 and ID+E 63/100,000 children). Cumulative incidence for DEE was 169/100,000 children (95% CI 144-199) and that for ID+E was 125/100,000 children (95% CI 95.4-165). Cumulative incidence per 100,000 children was as follows: infantile epileptic spasms syndrome 58.2 (95% CI 45.0-75.3), epilepsy with myoclonic-atonic seizures 16.4 (95% CI 9.69-27.7), Lennox-Gastaut syndrome 13.2 (95% CI 4.1-41.9), and Dravet syndrome 5.1 (95% CI 2.1-12.2). Fifty/152 (33%) of children with DEE and 70/83 (84%) with ID+E could not be diagnosed with a known epilepsy syndrome. Discussion: Epilepsy and developmental impairment before the age of 16 years occurs in 1 in 340 children, with 1 in 590 having a DEE and 1 in 800 having ID+E. These individuals require significant health and community resources; therefore, these data will inform complex health service and education planning. Epidemiologic studies have focused on early childhood-onset DEEs. These do not fully reflect the burden of these disorders because 27% of DEEs and 70% of ID+E begin later, with seizure onset after the age of 3 years. Understanding the cumulative incidence of specific syndromes together with the broad group of DEEs is essential for the planning of therapeutic trials. Given trials focus on specific syndromes, there is a risk that effective therapies will not be developed for one-third of children with DEE.

Rates of Status Epilepticus and Sudden Unexplained Death in Epilepsy in People With Genetic Developmental and Epileptic Encephalopathies Donnan AM, Schneider AL, Russ-Hall S, Churilov L, Scheffer IE. Neurology. 2023;100(16): e1712-e1722. doi:10.1212/WNL.0000000000207080 Background and Objectives: The genetic developmental and epileptic encephalopathies (DEEs) comprise a large group of severe epilepsy syndromes, with a wide phenotypic spectrum. Currently, the rates of convulsive status epilepticus (CSE), nonconvulsive status epilepticus (NCSE), and sudden unexplained death in epilepsy (SUDEP) in these diseases are not well understood. We aimed to describe the proportions of patients with frequently observed genetic DEEs who developed CSE, NCSE, mortality, and SUDEP. Understanding the risks of these serious presentations in each genetic DEE will enable earlier diagnosis and appropriate management. Methods: In this retrospective analysis of patients with a genetic DEE, we estimated the proportions with CSE, NCSE, and SUDEP and the overall and SUDEP-specific mortality rates for each genetic diagnosis. We included patients with a pathogenic variant in the genes SCN1A, SCN2A, SCN8A, SYNGAP1, NEXMIF, CHD2, PCDH19, STXBP1, GRIN2A, KCNT1, and KCNQ2 and with Angelman syndrome (AS). Results: The cohort comprised 510 individuals with a genetic DEE, in whom we observed CSE in 47% and NCSE in 19%. The highest proportion of CSE occurred in patients with SCN1A-associated DEEs, including 181/203 (89%; 95% CI 84-93) patients with Dravet syndrome and 8/15 (53%; 95% CI 27-79) non-Dravet SCN1A-DEEs. CSE was also notable in patients with pathogenic variants in KCNT1 (6/10; 60%; 95% CI 26-88) and SCN2A (8/15; 53%; 95% CI 27-79). NCSE was common in patients with non-Dravet SCN1A-DEEs (8/15; 53%; 95% CI 27-79) and was notable in patients with CHD2-DEEs (6/14; 43%; 95% CI 18-71) and AS (6/19; 32%; 95% CI 13-57). There were 42/510 (8%) deaths among the cohort, producing a mortality rate of 6.1 per 1,000 person-years (95% CI 4.4-8.3). Cases of SUDEP accounted for 19/42 (48%) deaths. Four genes were associated with SUDEP: SCN1A, SCN2A, SCN8A, and STXBP1. The estimated SUDEP rate was 2.8 per 1,000 person-years (95% CI 1.6-4.3). Discussion: We showed that proportions of patients with CSE, NCSE, and SUDEP differ for commonly encountered genetic DEEs. The estimates for each genetic DEE studied will inform early diagnosis and management of status epilepticus and SUDEP and inform disease-specific counseling for patients and families in this high-risk group of conditions.

O’Brien T, Perucca P, Ge Z, Anderson A. Applications for Deep Learning in Epilepsy Genetic Research

Epilepsy is a group of brain disorders characterised by an enduring predisposition to generate unprovoked seizures. Fuelled by advances in sequencing technologies and computational approaches, more than 900 genes have now been implicated in epilepsy. The development and optimisation of tools and methods for analysing the vast quantity of genomic data is a rapidly evolving area of research. Deep learning (DL) is a subset of machine learning (ML) that brings opportunity for novel investigative strategies that can be harnessed to gain new insights into the genomic risk of people with epilepsy. DL is being harnessed to address limitations in accuracy of long-read sequencing technologies, which improve on short-read methods. Tools that predict the functional consequence of genetic variation can represent breaking ground in addressing critical knowledge gaps, while methods that integrate independent but complimentary data enhance the predictive power of genetic data. We provide an overview of these DL tools and discuss how they may be applied to the analysis of genetic data for epilepsy research.

Social Determinants of Genetics Referral and Completion Rates Among Child Neurology Patients

Objective

To investigate clinical, social, and systems-level determinants predictive of genetics clinic referral and completion of genetics clinic visits among child neurology patients.

Methods

Electronic health record data were extracted from patients 0-18 years old who were evaluated in child neurology clinics at a single tertiary care institution between July 2018 to January 2020. Variables aligned with the Health Equity Implementation Framework. Referral and referral completion rates to genetics and cardiology clinics were compared among Black vs White patients using bivariate analysis. Demographic variables associated with genetics clinic referral and visit completion were identified using logistic regressions.

Results

In a cohort of 11,371 child neurology patients, 304 genetics clinic referrals and 82 cardiology clinic referrals were placed. In multivariate analysis of patients with Black or White ethnoracial identity (n=10,601), genetics clinic referral rates did not differ by race, but were significantly associated with younger age, rural address, neurodevelopmental disorder diagnosis, number of neurology clinic visits, and provider type. The only predictors of genetics clinic visit completion number of neurology clinic visits and race/ethnicity, with White patients being twice as likely as Black patients to complete the visit. Cardiology clinic referrals and visit completion did not differ by race/ethnicity.

Interpretation

Although race/ethnicity was not associated with differences in genetics clinic referral rates, White patients were twice as likely as Black patients to complete a genetics clinic visit after referral. Further work is needed to determine whether this is due to systemic/structural racism, differences in attitudes toward genetic testing, or other factors.

Evaluation of the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in infantile epilepsy (Gene-STEPS): an international, multicentre, pilot cohort study

BACKGROUND

Most neonatal and infantile-onset epilepsies have presumed genetic aetiologies, and early genetic diagnoses have the potential to inform clinical management and improve outcomes. We therefore aimed to determine the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in this population.

METHODS

We conducted an international, multicentre, cohort study (Gene-STEPS), which is a pilot study of the International Precision Child Health Partnership (IPCHiP). IPCHiP is a consortium of four paediatric centres with tertiary-level subspecialty services in Australia, Canada, the UK, and the USA. We recruited infants with new-onset epilepsy or complex febrile seizures from IPCHiP centres, who were younger than 12 months at seizure onset. We excluded infants with simple febrile seizures, acute provoked seizures, known acquired cause, or known genetic cause. Blood samples were collected from probands and available biological parents. Clinical data were collected from medical records, treating clinicians, and parents. Trio genome sequencing was done when both parents were available, and duo or singleton genome sequencing was done when one or neither parent was available. Site-specific protocols were used for DNA extraction and library preparation. Rapid genome sequencing and analysis was done at clinically accredited laboratories, and results were returned to families. We analysed summary statistics for cohort demographic and clinical characteristics and the timing, diagnostic yield, and clinical impact of rapid genome sequencing.

FINDINGS

Between Sept 1, 2021, and Aug 31, 2022, we enrolled 100 infants with new-onset epilepsy, of whom 41 (41%) were girls and 59 (59%) were boys. Median age of seizure onset was 128 days (IQR 46-192). For 43 (43% [binomial distribution 95% CI 33-53]) of 100 infants, we identified genetic diagnoses, with a median time from seizure onset to rapid genome sequencing result of 37 days (IQR 25-59). Genetic diagnosis was associated with neonatal seizure onset versus infantile seizure onset (14 [74%] of 19 vs 29 [36%] of 81; p=0·0027), referral setting (12 [71%] of 17 for intensive care, 19 [44%] of 43 non-intensive care inpatient, and 12 [28%] of 40 outpatient; p=0·0178), and epilepsy syndrome (13 [87%] of 15 for self-limited epilepsies, 18 [35%] of 51 for developmental and epileptic encephalopathies, 12 [35%] of 34 for other syndromes; p=0·001). Rapid genome sequencing revealed genetic heterogeneity, with 34 unique genes or genomic regions implicated. Genetic diagnoses had immediate clinical utility, informing treatment (24 [56%] of 43), additional evaluation (28 [65%]), prognosis (37 [86%]), and recurrence risk counselling (all cases).

INTERPRETATION

Our findings support the feasibility of implementation of rapid genome sequencing in the clinical care of infants with new-onset epilepsy. Longitudinal follow-up is needed to further assess the role of rapid genetic diagnosis in improving clinical, quality-of-life, and economic outcomes.

FUNDING

American Academy of Pediatrics, Boston Children's Hospital Children's Rare Disease Cohorts Initiative, Canadian Institutes of Health Research, Epilepsy Canada, Feiga Bresver Academic Foundation, Great Ormond Street Hospital Charity, Medical Research Council, Murdoch Children's Research Institute, National Institute of Child Health and Human Development, National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre, One8 Foundation, Ontario Brain Institute, Robinson Family Initiative for Transformational Research, The Royal Children's Hospital Foundation, University of Toronto McLaughlin Centre.

Review and standard operating procedures for collection of biospecimens and analysis of biomarkers in new onset refractory status epilepticus

New onset refractory status epilepticus (NORSE), including its subtype with a preceding febrile illness known as febrile infection-related epilepsy syndrome (FIRES), is one of the most severe forms of status epilepticus. The exact causes of NORSE are currently unknown, and there is so far no disease-specific therapy. Identifying the underlying pathophysiology and discovering specific biomarkers, whether immunologic, infectious, genetic, or other, may help physicians in the management of patients with NORSE. A broad spectrum of biomarkers has been proposed for status epilepticus patients, some of which were evaluated for patients with NORSE. Nonetheless, none has been validated, due to significant variabilities in study cohorts, collected biospecimens, applied analytical methods, and defined outcome endpoints, and to small sample sizes. The NORSE Institute established an open NORSE/FIRES biorepository for health-related data and biological samples allowing the collection of biospecimens worldwide, promoting multicenter research and sharing of data and specimens. Here, we suggest standard operating procedures for biospecimen collection and biobanking in this rare condition. We also propose criteria for the appropriate use of previously collected biospecimens. We predict that the widespread use of standardized procedures will reduce heterogeneity, facilitate the future identification of validated biomarkers for NORSE, and provide a better understanding of the pathophysiology and best clinical management for these patients.