Genetic diagnoses in epilepsy: The impact of dynamic exome analysis in a pediatric cohort.

OBJECTIVE: We evaluated the yield of systematic analysis and/or reanalysis of whole exome sequencing (WES) data from a cohort of well-phenotyped pediatric patients with epilepsy and suspected but previously undetermined genetic etiology. METHODS: We identified and phenotyped 125 participants with pediatric epilepsy. Etiology was unexplained at the time of enrollment despite clinical testing, which included chromosomal microarray (57 patients), epilepsy gene panel (n = 48), both (n = 28), or WES (n = 8). Clinical epilepsy diagnoses included developmental and epileptic encephalopathy (DEE), febrile infection-related epilepsy syndrome, Rasmussen encephalitis, and other focal and generalized epilepsies. We analyzed WES data and compared the yield in participants with and without prior clinical genetic testing. RESULTS: Overall, we identified pathogenic or likely pathogenic variants in 40% (50/125) of our study participants. Nine patients with DEE had genetic variants in recently published genes that had not been recognized as epilepsy-related at the time of clinical testing (FGF12, GABBR1, GABBR2, ITPA, KAT6A, PTPN23, RHOBTB2, SATB2), and eight patients had genetic variants in candidate epilepsy genes (CAMTA1, FAT3, GABRA6, HUWE1, PTCHD1). Ninety participants had concomitant or subsequent clinical genetic testing, which was ultimately explanatory for 26% (23/90). Of the 67 participants whose molecular diagnoses were "unsolved" through clinical genetic testing, we identified pathogenic or likely pathogenic variants in 17 (25%). SIGNIFICANCE: Our data argue for early consideration of WES with iterative reanalysis for patients with epilepsy, particularly those with DEE or epilepsy with intellectual disability. Rigorous analysis of WES data of well-phenotyped patients with epilepsy leads to a broader understanding of gene-specific phenotypic spectra as well as candidate disease gene identification. We illustrate the dynamic nature of genetic diagnosis over time, with analysis and in some cases reanalysis of exome data leading to the identification of disease-associated variants among participants with previously nondiagnostic results from a variety of clinical testing strategies.

PCDH19-related epilepsy is associated with a broad neurodevelopmental spectrum.

OBJECTIVE: To characterize the features associated with PCDH19-related epilepsy, also known as "female-limited epilepsy." METHODS: We analyzed data from participants enrolled in the PCDH19 Registry, focusing on the seizure-related, developmental, neurobehavioral, and sleep-related features. We evaluated variants for pathogenicity based on previous reports, population databases, and in silico predictions, and included individuals with pathogenic or potentially pathogenic variants. We performed a retrospective analysis of medical records and administered a targeted questionnaire to characterize current or past features in probands and genotype-positive family members. RESULTS: We included 38 individuals with pathogenic or potentially pathogenic variants in PCDH19: 21 de novo, 5 maternally inherited, 7 paternally inherited, and 5 unknown. All 38 had epilepsy; seizure burden varied, but typical features of clustering of seizures and association with fever were present. Thirty individuals had intellectual disability (ID), with a wide range of severity reported; notably, 8/38 (22%) had average intellect. Behavioral and sleep dysregulation were prominent, in 29/38 (76%) and 20/38 (53%), respectively. Autistic features were present in 22/38 (58%), of whom 12 had a formal diagnosis of autism spectrum disorder. We had additional data from 5 genotype-positive mothers, all with average intellect and 3 with epilepsy, and from 1 genotype-positive father. SIGNIFICANCE: Our series represents a robust cohort with carefully curated PCDH19 variants. We observed seizures as a core feature with a range of seizure types and severity. Whereas the majority of individuals had ID, we highlight the possibility of average intellect in the setting of PCDH19-related epilepsy. We also note the high prevalence and severity of neurobehavioral phenotypes associated with likely pathogenic variants in PCDH19. Sleep dysregulation was also a major area of concern. Our data emphasize the importance of appropriate referrals for formal neuropsychological evaluations as well as the need for formal prospective studies to characterize the PCDH19-related neurodevelopmental syndrome in children and their genotype-positive parents.

Compound heterozygosity with PRRT2: Pushing the phenotypic envelope in genetic epilepsies.

PRRT2 pathogenic variants have been described in benign familial infantile epilepsy, episodic ataxia, paroxysmal kinesigenic dyskinesia, and hemiplegic migraines. We describe a patient with compound heterozygous variants, infantile epilepsy with status epilepticus, paroxysmal dyskinesia and episodic ataxia. Testing revealed a pathogenic PRRT2 duplication (c.649dupC), and a likely pathogenic missense variant (c.916G>A). His presentation meets the severe phenotypic category with a combination of at least 3 neurological symptoms: seizures and status epilepticus, prolonged episodic ataxia, and paroxysmal dyskinesia. This further expands the clinical findings related to PRRT2, and suggests that compound heterozygous variants could confer a severe phenotype.

Psychiatric disorders in clinical genetics I: Addressing family histories of psychiatric illness.

This is the first article of a two-part professional development series addressing genetic counseling for personal and family histories of psychiatric disorders. It is based on an Educational Breakout Session presented by the Psychiatric Special Interest Group of the National Society of Genetic Counselors at the 2006 Annual Education Conference. This article examines issues that arise in addressing family histories of psychiatric illness, while the second article in the series considers the generation and provision of individualized recurrence risks for psychiatric disorders. In this article we discuss the importance of managing uncertainty for affected individuals and their close family members who have been referred to genetics for a number of different indications. We then use four simulated cases to make recommendations about the scope and timing of discussions related to the psychiatric family history.

Psychiatric disorders in clinical genetics II: Individualizing recurrence risks.

This is the second article of a two-part professional development series on genetic counseling for personal and family histories of psychiatric disorders. It is based on an Educational Breakout Session presented by The Psychiatric Special Interest Group of the National Society of Genetic Counselors at the 2006 Annual Education Conference. While the first article in this two part series dealt with addressing family histories of psychiatric disorders in clinical practice, the following discussion deals with the generation and provision of individualized recurrence risks for psychiatric disorders, based on empiric risk data. We present four cases that illustrate important components of and process for generating individualized risk assessment for family histories of psychiatric disorders.

Communicative competence in parents of children with autism and parents of children with specific language impairment.

While the primary language deficit in autism has been thought to be pragmatic, and in specific language impairment (SLI) structural, recent research suggests phenomenological and possibly genetic overlap between the two syndromes. To compare communicative competence in parents of children with autism, SLI, and down syndrome (DS), we used a modified pragmatic rating scale (PRS-M). Videotapes of conversational interviews with 47 autism, 47 SLI, and 21 DS parents were scored blind to group membership. Autism and SLI parents had significantly lower communication abilities than DS parents. Fifteen percent of the autism and SLI parents showed severe deficits. Our results suggest that impaired communication is part of the broader autism phenotype and a broader SLI phenotype, especially among male family members.

A Model Program for Translational Medicine in Epilepsy Genetics.

Recent technological advances in gene sequencing have led to a rapid increase in gene discovery in epilepsy. However, the ability to assess pathogenicity of variants, provide functional analysis, and develop targeted therapies has not kept pace with rapid advances in sequencing technology. Thus, although clinical genetic testing may lead to a specific molecular diagnosis for some patients, test results often lead to more questions than answers. As the field begins to focus on therapeutic applications of genetic diagnoses using precision medicine, developing processes that offer more than equivocal test results is essential. The success of precision medicine in epilepsy relies on establishing a correct genetic diagnosis, analyzing functional consequences of genetic variants, screening potential therapeutics in the preclinical laboratory setting, and initiating targeted therapy trials for patients. The authors describe the structure of a comprehensive, pediatric Epilepsy Genetics Program that can serve as a model for translational medicine in epilepsy.

Autism-related language, personality, and cognition in people with absolute pitch: results of a preliminary study.

Reports of a relatively high prevalence of absolute pitch (AP) in autistic disorder suggest that AP is associated with some of the distinctive cognitive and social characteristics seen in autism spectrum disorders. Accordingly we examined cognition, personality, social behavior, and language in 13 musicians with strictly defined AP (APS) and 33 musician controls (MC) without AP using standardized interviews and tests previously applied to identify the broad autism phenotype seen in the relatives of autistic probands. These included the Pragmatic Rating Scale (PRS) (social aspects of language) the Personality Assessment Schedule (PAS) (rigidity, aloofness, anxiety/worry, hypersensitivity), and WAIS performance subtests (PIQ). On the basis of their behavior in the interviews, subjects were classified as socially eccentric, somewhat eccentric, or not eccentric. Forty-six percent of the APS, but only 15% of the MC, were classified as socially eccentric (p < .03). APS but not MC showed higher scores on block design than on the other PIQ tests (p < .06), a PIQ pattern seen in autism spectrum disorders. Although APS and MC did not differ significantly on other measures it is of note that APS mean scores on the PRS and PAS (5.69, 4.92) were almost twice as high as those for the MC (3.03, 2.45). Thus, musicians with AP show some of the personality, language, and cognitive features associated with autism. Piecemeal information processing, of which AP is an extreme and rare example, is characteristic of autism and may be associated as well with subclinical variants in language and behavior. We speculate that the gene or genes that underlie AP may be among the genes that contribute to autism.

Parental interest in a genetic risk assessment test for autism spectrum disorders.

To better understand parental opinions regarding the diagnostic process and use of genetic testing to assess risk for autism spectrum disorders (ASDs) in the younger siblings of affected children in the Unites States, we conducted a survey of parents who had at least one child with ASD. A total of 162 surveys were completed anonymously using an Internet-based survey tool. The mean reported time to ASD diagnosis and age at diagnosis were 35.2 months and 56.6 months, respectively. Seventy-two percent of parents felt there was a delay in diagnosis. Most parents indicated they would want to pursue genetic testing if a test were available that could identify risk in a younger sibling (80%). Earlier evaluation/intervention, closer monitoring, and lessened anxiety were reasons cited for testing. Our survey indicates most parents would pursue genetic risk assessment testing in children at high risk for ASD.

Clinical genetic testing for patients with autism spectrum disorders.

BACKGROUND: Multiple lines of evidence indicate a strong genetic contribution to autism spectrum disorders (ASDs). Current guidelines for clinical genetic testing recommend a G-banded karyotype to detect chromosomal abnormalities and fragile X DNA testing, but guidelines for chromosomal microarray analysis have not been established. PATIENTS AND METHODS: A cohort of 933 patients received clinical genetic testing for a diagnosis of ASD between January 2006 and December 2008. Clinical genetic testing included G-banded karyotype, fragile X testing, and chromosomal microarray (CMA) to test for submicroscopic genomic deletions and duplications. Diagnostic yield of clinically significant genetic changes was compared. RESULTS: Karyotype yielded abnormal results in 19 of 852 patients (2.23% [95% confidence interval (CI): 1.73%-2.73%]), fragile X testing was abnormal in 4 of 861 (0.46% [95% CI: 0.36%-0.56%]), and CMA identified deletions or duplications in 154 of 848 patients (18.2% [95% CI: 14.76%-21.64%]). CMA results for 59 of 848 patients (7.0% [95% CI: 5.5%-8.5%]) were considered abnormal, which includes variants associated with known genomic disorders or variants of possible significance. CMA results were normal in 10 of 852 patients (1.2%) with abnormal karyotype due to balanced rearrangements or unidentified marker chromosome. CMA with whole-genome coverage and CMA with targeted genomic regions detected clinically relevant copy-number changes in 7.3% (51 of 697) and 5.3% (8 of 151) of patients, respectively, both higher than karyotype. With the exception of recurrent deletion and duplication of chromosome 16p11.2 and 15q13.2q13.3, most copy-number changes were unique or identified in only a small subset of patients. CONCLUSIONS: CMA had the highest detection rate among clinically available genetic tests for patients with ASD. Interpretation of microarray data is complicated by the presence of both novel and recurrent copy-number variants of unknown significance. Despite these limitations, CMA should be considered as part of the initial diagnostic evaluation of patients with ASD.