Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes.

PURPOSE: This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program. METHODS: Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes. RESULTS: Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases). CONCLUSION: Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation and by providing HiFi variant (SNV/SV) resources from >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.

Hypotonia and intellectual disability without dysmorphic features in a patient with PIGN-related disease.

BACKGROUND: Defects in the human glycosylphosphatidylinositol anchor biosynthetic pathway are associated with inherited glycosylphosphatidylinositol (GPI)-deficiencies characterized by a broad range of clinical phenotypes including multiple congenital anomalies, dysmorphic faces, developmental delay, hypotonia, and epilepsy. Biallelic variants in PIGN, encoding phosphatidylinositol-glycan biosynthesis class N have been recently associated with multiple congenital anomalies hypotonia seizure syndrome. CASE PRESENTATION: Our patient is a 2 year old male with hypotonia, global developmental delay, and focal epilepsy. Trio whole-exome sequencing revealed heterozygous variants in PIGN, c.181G > T (p.Glu61*) and c.284G > A (p.Arg95Gln). Analysis of FLAER and anti-CD59 by flow-cytometry demonstrated a shift in this patient's granulocytes, confirming a glycosylphosphatidylinositol-biosynthesis defect, consistent with PIGN-related disease. CONCLUSIONS: To date, a total of 18 patients have been reported, all but 2 of whom have congenital anomalies and/or obvious dysmorphic features. Our patient has no significant dysmorphic features or multiple congenital anomalies, which is consistent with recent reports linking non-truncating variants with a milder phenotype, highlighting the importance of functional studies in interpreting sequence variants.

PCDH19-related epileptic encephalopathy in a male mosaic for a truncating variant.

Variants in the X-linked gene PCDH19 are associated with early infantile epileptic encephalopathy-9. This unusual condition spares hemizygous males except for psychiatric and behavioral abnormalities, and for this reason is also known as female limited epilepsy. Some cases are due to de novo PCDH19 variants, but may also be paternally inherited. Our patient is a 6-year-old male with epileptic encephalopathy. Exome sequencing revealed apparent heterozygosity in PCDH19 for a novel nonsense variant, c.605C>A (p.Ser202*), inconsistent with expectations for a male. Testing of other tissues revealed a mixture of mutant and normal alleles. These results are consistent with somatic mosaicism for p.Ser202*. This is the second male with somatic mosaicism for PCDH19 deficiency, providing further support for cellular interference as the pathogenic mechanism for this condition, which leads to this unusual mode of inheritance in which females are more severely affected than males. © 2016 Wiley Periodicals, Inc.

Factors Associated With Growth in Patients Treated With the Classic Ketogenic Diet for Drug-Resistant Epilepsy.

BACKGROUND: Suboptimal growth and malnutrition are often cited as complications of ketogenic diet therapy in patients with drug-resistant epilepsy; however, there is conflicting evidence on the factors that contribute to growth. METHODS: This is an observational, case-based study to evaluate growth in patients with drug-resistant epilepsy treated with the classic ketogenic diet for at least 12 months. Age, gender, height, weight, and body mass index (BMI) were collected at baseline and epilepsy clinic standard-of-care visits (one month, six months, and 12 months after diet initiation). Dietary intake and laboratory measures including glucose, bicarbonate, and beta-hydroxybutyrate were also collected. RESULTS: 119 patients were included. After ketogenic diet initiation, there was a significant fall in height z score from baseline to 12 months (-0.15, P = 0.001) but no other significant changes in weight, weight-for-length/BMI, or height z scores were noted between any time points within the 12 months after diet initiation. When separated by age, height z score changes were limited to those aged zero to three years. This was accompanied by a significant decrease in energy intake 12 months after treatment in this age group. When separated by diet route, weight z scores at each time point were significantly lower in the group eating by mouth than tube. CONCLUSIONS: Our study provides further evidence that the classic ketogenic diet impacts growth. Our population demonstrated restriction in linear growth in those aged zero to three years, which correlated with declines in energy intake, and weight declines limited to patients fed by mouth.

Efficacy and Tolerability of Ultra Rapid Duty Cycling Vagus Nerve Stimulation for Medically Refractory Absence Seizures.

BACKGROUND: Significant knowledge gap exists on vagus nerve stimulation (VNS) efficacy and tolerability in medically refractory absence seizures (MRAS). This retrospective review of patients with MRAS aims to narrow this knowledge gap by comparing ultra rapid duty cycling ([URDC] ON time seven seconds, OFF time 0.2 minutes) with less frequent stimulations of rapid duty cycling (RDC, OFF time <1.1 minutes) and normal duty cycling (NDC, OFF time ≥1.1 minutes). METHODS: Patients with MRAS aged less than 21 years who underwent VNS implantation were identified. Patient demographics, antiepileptic medications, seizure types, frequency, VNS parameters, outcomes of seizure reduction rate (SRR), and seizure freedom were extracted and compared among NDC, RDC, and URDC patient cohorts. RESULTS: Thirty-six patients with MRAS were identified. After a mean follow-up of 32.6 months, responder rate ([RR], SRR ≥50%) for URDC was 80% for absence seizures and 80% for all seizure types versus 66.67% and 66.77% for NDC and 78.57% and 57.14% for RDC, respectively. Six of 10 patients (60%) on URDC achieved complete seizure freedom. A higher rate of subjective improvement in academic performance, attention, and developmental gain was noted in the URDC group. Patients on URDC tolerated higher output current (mean 3.025 mA) with minimal side effects but required a battery change sooner. CONCLUSIONS: VNS is a safe and effective nonpharmacologic management choice in patients with MRAS. The data presented demonstrate that the combination of URDC and high output current provides better RR and seizure freedom. Apart from a reduced battery life, this parameter modality seems to be well-tolerated.

The use of virtual tools in narrowing the impact of health disparities in neurology.

The concept of Epilepsy Treatment Gap (ETG) refers to the proportion of people with epilepsy who are not being appropriately treated. The ETG in the USA approaches 10%, with historically underserved populations and rural populations disproportionately affected. The ETG in Low-and Middle-Income Countries (LMIC) is reported to be 5-10 times higher than in high-income countries. The growing availability of reliable internet access offers a unique opportunity to provide better care to children and adults with epilepsy. In this paper we explore various telehealth (TH) initiatives that have leveraged the availability of easy and free access to an internet connection in reducing the ETG in underserved regions of the world. We describe several interventions targeted to reach patients and providers in rural areas of the United States and in LMIC. First, we examine initiatives that were developed to improve patient access to coordinated care and education regarding epilepsy and seizures. Next, we describe an intervention designed to improve knowledge of epilepsy diagnosis and treatment for providers in LMIC. We conclude with a brief overview of the use of virtual tools in diminishing the ETG.

The efficacy and tolerability of auto-stimulation-VNS in children with Lennox-Gastaut syndrome.

OBJECTIVE: Lennox-Gastaut syndrome (LGS) is a severe drug-resistant epilepsy (DRE) of childhood. The Vagus Nerve Stimulator (VNS) is established as a safe and effective treatment for DRE. This study assesses efficacy and tolerability of the auto-stimulation VNS models in pediatric patients with LGS. METHODS: This is a retrospective chart review of a cohort of pediatric patients (Age 1-18 years old) with LGS implanted with an auto-stimulation VNS model at a single level four pediatric epilepsy center. Patient responder's rate was measured as seizure reduction over baseline and improvements in five quality-of-life measures as reported by the patients and families. Efficacy and tolerability were assessed at 1, 3, 6, 12, 18 and 24 months compared to baseline. RESULTS: This cohort includes 71 consecutive children with Lennox-Gastaut syndrome who underwent implantation with one of two models of the auto-stimulation VNS. The average age of the children at implantation was 20.82 months. Of those patients, 55 % of patients achieved greater than 50 % seizure reduction at six months, 67.7 % at 12 months, and 65 % at 24 months. At 12 months 11 % of the patients were completely seizure free and at 24 months 17 % were seizure free. By 24 months post implantation most of the patient families reported at least a 50 % improvement rate in one or more of the quality-of-life measures. The most commonly reported adverse events were dysphonia, paresthesia, and shortness of breath, all of which were tolerated and subsided by 24 months. SIGNIFICANCE: This study provides evidence that VNS models with the auto-stimulation paradigm based on detection of tachycardia are well tolerated and effective in a pediatric population with LGS. Furthermore, this study shows that for this population, the auto-stimulation models of the VNS may provide additional benefits over the earlier VNS versions.

Combined use of the ketogenic diet and vagus nerve stimulation in pediatric drug-resistant epilepsy.

Objective: Patients with drug-resistant epilepsy (DRE) pose considerable management challenges for patients, their families, and providers. Both the vagus nerve stimulator (VNS) and the ketogenic diet (KD) have been shown to be safe and effective in treating DRE. Nevertheless, information is lacking regarding treatment with combination of both modalities. This study reports the efficacy and tolerability of combining VNS and KD in a pediatric cohort with intractable epilepsy. Methods: This is a retrospective review of 33 patients (0-17 years) with DRE treated with VNS and KD at a single pediatric level IV epilepsy center. We compared seizure reduction rates for each patient at baseline and at every clinic visit for 24 months after adding the second nonpharmacological therapy. The frequency of adverse events on the combined therapy was collected to assess safety and tolerability. Results: There were a total of 170 visits for all patients while on the combined therapy. At 88% (95% CI: 83%-93%) of the visits, patients reported some reduction in seizure frequency. The proportion of patients reporting a greater than 50% seizure reduction over all visits was 62% (95% CI: 55%-69%). The proportion of a patient's visits with at least a greater than 50% reduction in seizure frequency had a median of 71% (IQR 33%-100%). Continued improvement was seen over time of combined treatment; for every one-unit time unit change (one month), there was a 6% increase in the odds of having a reduction in seizure frequency of >50% (OR = 1.06, 95% CI: 1.01-1.11). Significance: This study shows that combining the VNS and KD in patients with drug-resistant epilepsy is well tolerated and reduces seizure frequency more than either one modality used alone and that the benefits in terms of seizure reduction continue to increase with the length of treatment.

Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing.

Status epilepticus is not rare in critically ill intensive care unit patients, but its diagnosis is often delayed or missed. The mortality for convulsive status epilepticus is dependent on the underlying aetiologies and the age of the patients and thus varies from study to study. In this context, effective molecular diagnosis in a pediatric patient with a genetically heterogeneous phenotype is essential. Homozygous or compound heterozygous variants in KPTN have been recently associated with a syndrome typified by macrocephaly, neurodevelopmental delay, and seizures. We describe a comprehensive investigation of a 9-yr-old male patient who was admitted to the intensive care unit, with focal epilepsy, static encephalopathy, autism spectrum disorder, and macrocephaly of unknown etiology, who died of status epilepticus. Clinical whole-genome sequencing revealed compound heterozygous variants in the KPTN gene. The first variant is a previously characterized 18-bp in-frame duplication (c.714_731dup) in exon 8, resulting in the protein change p.Met241_Gln246dup. The second variant, c.394 + 1G > A, affects the splice junction of exon 3. These results are consistent with a diagnosis of autosomal recessive KPTN-related disease. This is the fourth clinical report for KPTN deficiency, providing further evidence of a wider range of severity.

The Efficacy and Safety of Rapid Cycling Vagus Nerve Stimulation in Children With Intractable Epilepsy.

PURPOSE: Vagus nerve stimulation (VNS) is an effective adjunctive therapy for drug-resistant epilepsy. Nevertheless, information is lacking regarding optimization of stimulation parameters to improve efficacy. Our study examines the safety and efficacy of rapid duty cycle VNS (OFF time ≤1.1 minute keeping duty cycle less than 50%) in pediatric cohort with intractable epilepsy. METHODS: Retrospective chart review of 50 patients (one to 17 years) with drug-resistant epilepsy treated with VNS between 2010 and 2015 at a single pediatric epilepsy center. Safety and tolerability data were aggregated across all patient visits to determine frequency of adverse events between differing duty cycles. We also compared seizure reduction rates for each patient at (1) last regular duty cycle visit, (2) first rapid duty cycle visit, and (3) last recorded rapid duty cycle visit. RESULTS: Rapid duty cycle was well tolerated, with no adverse events reported in 96.6% patient encounters. At the last visit before switching to rapid duty cycle 45.5% patients were showing response to VNS (seizure reduction rates ≥50%). This rate increased to 77.3% after switching to rapid duty cycle and remained at 77.4% at the last rapid duty cycle visit. Fifteen patients (34.1%) became responders to VNS after switching to rapid cycling; another 19 (43.2%) maintained their response with mostly improved seizure reduction rates. In only a few instances, responders became nonresponders after switching to rapid duty cycle. CONCLUSIONS: Rapid duty cycle VNS is probably safe and well tolerated; it may also be more efficacious than regular cycling VNS in some patients. This study highlights the necessity of prospective, long-term, double-blinded studies for understanding the advantages of this VNS modality.

Initiating the ketogenic diet in infants with treatment refractory epilepsy while maintaining a breast milk diet.

PURPOSE: The ketogenic diet has been found to be safe and effective in the treatment of drug resistant epilepsy in childhood. The age range of children undergoing this treatment has steadily been going down. There is strong evidence that it is a safe alternative in infants with drug resistant seizures. The American Academy of Pediatrics strongly supports continuing a breast milk diet until infants are at least six months of age. The purpose of this study is to evaluate the safety and efficacy of the ketogenic diet in infants while maintaining a breast milk diet. METHOD: This is a cohort study of 9 infants between the ages of 1 and 13 months with drug resistant epilepsy treated with the ketogenic diet while maintained on breast milk. The data from the first two patients was gathered retrospectively while the other seven were studied prospectively. RESULTS: We show that all nine infants achieved and maintained ketosis effectively. While one infant had no change in seizure frequency, three were seizure free at the first follow-up visit and four had a burden of seizure reduction greater than 50%. The diet was overall well tolerated, although one child required a hospital stay for dehydration and metabolic acidosis. CONCLUSION: The ketogenic diet can be safely and effectively initiated in infants while continuing human breast milk feedings.

Safety and tolerability of adjunctive lacosamide in a pediatric population with focal seizures - An open-label trial.

PURPOSE: To evaluate safety and tolerability of adjunctive lacosamide in children with focal seizures. METHODS: Patients were eligible for this open-label, fixed-titration trial (SP0847; NCT00938431) if aged 1 month-17 years with focal seizures taking 1-3 antiepileptic drugs. Findings from Cohort 1, aged 5-11 years, who received lacosamide ≤8 mg/kg/day, informed dosing for age-based cohorts 2-5, who then received ≤12 mg/kg/day (≤600 mg/day). Oral lacosamide was initiated at 2 mg/kg/day (1 mg/kg bid) and uptitrated by 2 mg/kg/day/week to the maximum cohort-defined dose (maximum trial duration: 13 weeks). Patients who did not achieve the maximum cohort-defined dose were discontinued. RESULTS: Forty-seven patients (aged 6 months-≤17 years) enrolled (≥1 month-<4 years: n = 15; ≥4-<12 years: n = 23; ≥12-≤17 years: n = 9). 24/47 (51.1%) patients completed the trial at the maximum cohort-defined dose and 40/47 (85.1%) continued lacosamide in the extension trial. Treatment-emergent adverse events (TEAEs) were reported by 42/47 (89.4%) patients. The most common TEAEs (≥10% of patients) were vomiting (21.3%), diarrhea (14.9%), somnolence (12.8%), irritability, dizziness, and pyrexia (10.6% each). Twenty (42.6%) patients discontinued due to TEAEs, most commonly vomiting (8.5%), gait disturbance, dizziness, and somnolence (6.4% each). Six (12.8%) patients reported serious TEAEs, most commonly status epilepticus (3/47; 6.4%). CONCLUSION: This fixed-titration trial supports the safety of adjunctive lacosamide in children (aged 6 months-≤17 years) with focal seizures. The TEAE profile was generally consistent with that observed in trials in adults, and no new safety concerns were identified.

Electroclinical Features of Generalized Paroxysmal Fast Activity in Typical Absence Seizures.

PURPOSE: Generalized paroxysmal fast activity (GPFA) is a diffuse, paroxysmal, frontal predominant activity described in patients with generalized epilepsies. Studies specifically focusing on electroclinical features of typical absence seizures in children have not reported any GPFA-like features. We sought to identify GPFA in children with typical absence seizures, study its incidence, characteristic electroclinical features, and effect on their epilepsy. METHODS: We performed a retrospective review of electroencephalograms of children with diagnosis of absence epilepsy. A total of 173 subjects were identified. In subjects with GPFA on their electroencephalograms, GPFA characteristics were collected (i.e., predominant location, duration, amplitude, frequency, provocation factors, and if GPFA was followed by spike-wave discharges). In GPFA-positive subjects, further data sets were collected examining their demographics, duration of epilepsy, and pharmacoresponsiveness to epilepsy. RESULTS: Generalized paroxysmal fast activity was identified in 10 subjects (5.78%) with female to male ratio of 9:1. Median age of subjects was 17 years, and median duration of illness was 9.5 years. Mean maximum GPFA amplitude was 88.3 µV with posterior predominance in 9/10 subjects. Generalized paroxysmal fast activity frequency ranged between 11 and 20 Hz with duration of 1 to 4 seconds. Generalized paroxysmal fast activity was provoked with eye closure, hyperventilation, and photic stimulation. Antiseizure medications had no effect on GPFA, and epilepsy was well controlled in most subjects. CONCLUSIONS: Generalized paroxysmal fast activity is uncommon in children with typical absence seizures and has medium voltage, posterior predominance, and marked female preponderance. Generalized paroxysmal fast activity is seen during both pharmacoresponsive and drug-resistant epilepsy, and is not affected by antiseizure medications. It may serve as an independent marker of lifelong epilepsy.

Cerebral venous thrombosis after immune thrombocytopenic purpura and anti-D immune globulin therapy.

Cerebral venous thrombosis has multiple etiologies and a wide variety of clinical manifestations. This article reports on a young girl who developed cerebral venous thrombosis after intravenous anti-D immune globulin therapy for immune thrombocytopenic purpura. In this case, venous infarction was manifested by an unusual pattern of restricted diffusion limited to the corpus callosum. The cause of cerebral venous thrombosis in this patient may be related to both immune thrombocytopenia and immunoglobulin therapy.

Ketogenic Diet Decreases Emergency Room Visits and Hospitalizations Related to Epilepsy.

Background. Approximately, one-third of patients with epilepsy are refractory to pharmacological treatment which mandates extensive medical care and imposes significant economic burden on patients and their societies. This study intends to assess the impact of the treatment with ketogenic diet (KD) on reducing seizure-related emergency room visits and hospitalizations in children with refractory epilepsy. Methods. This is a retrospective review of children treated with the KD in one tertiary center. We compared a 12 months' period prior to KD with 12 months after the diet was started in regard to the number of emergency department (ED) visits, hospitalizations, and hospital days as well as their associated charges. Results. 37 patients (57% males) were included. Their ages at time of KD initiation were (4.0 ± 2.78) years. Twelve months after the KD initiation, the total number of ED visits was reduced by 36% with a significant decrease of associated charges (p = 0.038). The number of hospital admissions was reduced by 40% and the number of hospital days was reduced by 39%. The cumulative charges showed net cost savings after 9 months when compared to the prediet baseline. Conclusion. In children with refractory epilepsy, treatment with the ketogenic diet reduces the number of ED visits and hospitalizations and their corresponding costs.

Management of symptomatic cholelithiasis while on ketogenic diet: a case report.

INTRODUCTION: The ketogenic diet is a treatment modality used for patients with refractory epilepsy. Development of cholelithiasis while on the ketogenic diet is a potential side effect that has been described in the literature. There however have not been any reports on the outcomes of continuing the diet after cholecystectomy. PATIENT: We present a 5-year-old boy with history of pharmacologically intractable epilepsy that was well controlled on the ketogenic diet. He underwent laparoscopic cholecystectomy for the development of symptomatic cholelithiasis 12 months after the initiation of ketogenic diet for seizure control. RESULTS: Patient tolerated the surgery well and was able to continue the ketogenic diet postoperatively. DISCUSSION: There have been no reports describing the continuation of ketogenic diet after cholecystectomy. This child demonstrates the safety of the procedure and the ability to continue the ketogenic diet without further biliary or surgical complications.

Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders.

Neurodevelopmental disorders (NDDs) affect more than 3% of children and are attributable to single-gene mutations at more than 1000 loci. Traditional methods yield molecular diagnoses in less than one-half of children with NDD. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) can enable diagnosis of NDD, but their clinical and cost-effectiveness are unknown. One hundred families with 119 children affected by NDD received diagnostic WGS and/or WES of parent-child trios, wherein the sequencing approach was guided by acuity of illness. Forty-five percent received molecular diagnoses. An accelerated sequencing modality, rapid WGS, yielded diagnoses in 73% of families with acutely ill children (11 of 15). Forty percent of families with children with nonacute NDD, followed in ambulatory care clinics (34 of 85), received diagnoses: 33 by WES and 1 by staged WES then WGS. The cost of prior negative tests in the nonacute patients was $19,100 per family, suggesting sequencing to be cost-effective at up to $7640 per family. A change in clinical care or impression of the pathophysiology was reported in 49% of newly diagnosed families. If WES or WGS had been performed at symptom onset, genomic diagnoses may have been made 77 months earlier than occurred in this study. It is suggested that initial diagnostic evaluation of children with NDD should include trio WGS or WES, with extension of accelerated sequencing modalities to high-acuity patients.

The role of epilepsy surgery in the treatment of childhood epileptic encephalopathy.

Children with epileptic encephalopathy often have global impairment of brain function and frequent intractable seizures, which contribute further to their developmental disability. Many of these children have identifiable brain lesion on neurological imaging. In such cases, epilepsy surgery may be considered as a treatment option despite the lack of localized epileptic pattern on electroencephalogram (EEG). In this paper, we summarize the clinical features of epileptic encephalopathy syndromes and review the reported literature on the surgical approach to some of these disorders.

15q11.2 proximal imbalances associated with a diverse array of neuropsychiatric disorders and mild dysmorphic features.

Deletion within the proximal region of chromosome 15q11.2 between breakpoints 1 and 2 (BP1-BP2) has been proposed to be a risk factor for intellectual disability, seizure, and schizophrenia. However, the clinical significance of its reciprocal duplication is not clearly defined yet. We evaluated 1654 consecutive pediatric patients with various neurological disorders by high-resolution microarray-based comparative genomic hybridization. We identified 21 patients carrying 15q11.2 BP1-BP2 deletion and 12 patients carrying 15q11.2 BP1-BP2 duplication in this cohort, which represent 1.27% (21/1,654) and 0.7% (12/1,654) of the patients analyzed, respectively. Approximately 87.5% of the patients carrying the deletion and 80% of the patients carrying the duplication have developmental delay or intellectual disability. Other recurrent clinical features in these patients include mild dysmorphic features, autistic spectrum disorders, and epilepsy. Our observations provide further evidence in favor of a strong association of 15q11.2 BP1-BP2 deletion with a variety of neuropsychiatric disorders. The diversity of clinical findings in these patients expands the phe-notypic spectrum of individuals carrying the deletion. In addition, possible etiological effects of 15q11.2 BP1-BP2 duplication in neuropsychiatric disorders are proposed.