J Genet Counsel DOI 10.1007/s10897-015-9906-9

REVIEW PAPER

Review of Commercially Available Epilepsy Genetic Panels Chelsea Chambers 1,2 & Laura A. Jansen 1 & Radhika Dhamija 1,2

Received: 27 January 2015 / Accepted: 20 October 2015 # National Society of Genetic Counselors, Inc. 2015

Abstract Next generation sequencing panels have revolutionized the diagnostic approach to patients with epilepsy. There are several commercial epilepsy panels available. We assessed the list of genes tested and consent forms for epilepsy panels available at seven laboratories. The panels varied in the number of genes included (70–465 genes). In some panels, genes not currently associated with epilepsy were included (up to 4 % of panel content). The panels also included genes for lysosomal storage disorders (6–12 %), congenital disorders of glycosylation (0–8.5 %), metabolic disorders (3.5– 34 %), neurological syndromes (18–43 %) and multisystemic genetic syndromes (6.4–21 %). Informed consents differed significantly between laboratories ranging from basic information about genetic testing and possible results to information about insurance, genetic counseling and familial testing, and incidental findings. Our findings suggest that it is important to consider the range of genes offered on epilepsy panels and their predicted phenotypes in an effort toward improving the informed consent process. Keywords Next generation sequencing . Epilepsy . Genetic counselling Electronic supplementary material The online version of this article (doi:10.1007/s10897-015-9906-9) contains supplementary material, which is available to authorized users. * Radhika Dhamija [email protected] 1

Department of Neurology, University of Virginia, PO Box 800394, Charlottesville, VA, USA

2

Department of Pediatrics (Division of Genetics and Metabolism), University of Virginia, PO Box 800394, Charlottesville, VA, USA

Introduction Epidemiological studies have shown that approximately 40– 50 million people in the world have epilepsy and one-third of all epilepsy is medically intractable (Kwan et al. 2011). Evaluation of the genetic basis of intractable epilepsy is one of the most frequent referral indications in a Neurogenetics clinic. There has been rapid increase in our knowledge of epilepsy genetics in the last two decades (Scheffer 2014). Epilepsy can have an identifiable genetic cause in many patients previously thought to have an idiopathic form of epilepsy (Pong et al. 2011). In addition to single gene mutations causing epilepsy, we now know that a combination of mutations in multiple genes can also cause epilepsy (Pong et al. 2011). Epilepsy is also one of the protean manifestations of many dysmorphology and multisystemic genetic syndromes and often occurs in neurodegenerative diseases. Next-generation DNA sequencing, also referred to as massively parallel sequencing, is a high-throughput DNA sequencing technology that is capable of sequencing large numbers of genes in a single reaction. Next generation sequencing (NGS) panels are now used widely in clinical settings to try to identify genetics causes of epilepsy (de Koning et al. 2014) and have revolutionized the diagnostic approach to patients with intractable epilepsy. The results of these panels have helped clinicians make a diagnosis and solve the Bdiagnostic odyssey cases.^ They have also helped clinicians in prognostication, guiding treatment choices in some cases, and in providing appropriate genetic counseling to families. In a retrospective study from a tertiary Pediatric epilepsy center, the diagnostic rate of these epilepsy panels was found to be around 21 % (Wang et al. 2014). Over time these panels have become cheaper and turnaround time for results is also decreasing considerably. In some situations, an epilepsy panel is ordered as first-tier test for intractable epilepsy. There are numerous commercial epilepsy panels available and

Chambers, Jansen and Dhamija

according to Genetic Testing Registry in November 2014, there are over 100 different panels available. However, choosing a particular panel can often be challenging for clinicians. There are several considerations that one needs to keep in mind while choosing among the panels. Is having more genes in a panel always good? Are there any adult onset neurodegerative diseases included in the panel for which a different consent process needs to be taken? Are parental studies offered by the laboratories if variants of uncertain significance are identified?

Methods In order to better understand the current status of genetic testing for epilepsy, we assessed the list of genes tested and consent forms for comprehensive epilepsy NGS panels available at seven large US-based commonly used clinical laboratories (Transgenomics, Medical Neurogenetics, GeneDx, Athena, Emory Genetics, Greenwood Genetics and Courtagen) (December 2014). We initially chose laboratories with>100 genes on their epilepsy panel and then added GeneDx (with< 100 genes) based on its popularity in United States. All genes included in the panel were tabulated against their phenotype and the seven laboratories were compared. Twelve categories were made based on a combination of disease pathogenesis, different management strategies, and prognosis, key issues related to pretest counseling and to keep it consistent with the categories (of disorders included in the epilepsy panels) listed by the laboratories we studied. The genes were categorized in one of the following groups: 1) Single genes causing epilepsy and/or epileptic encephalopathy (e.g., channelopathies), 2) Probably associated with epilepsy (e.g., genes associated with epilepsy in animal models only), 3) Multisystemic genetic syndromes that can also cause seizures (e.g., cardiofacialcutaneous (CFC) syndrome), 4) Neurological syndromes (e.g., Joubert syndrome), 5) Metabolic disorders detected on core ACMG recommended newborn screening (Sweetman et al. 2006), 6) Metabolic disorders not detected on core ACMG recommended newborn screening, 7) Lysosomal disorders, 8) Congenital disorders of glycosylation, 9) Peroxisomal biogenesis disorders, 10) Genes important in pharmacogenomics, 11) Genes currently not known to cause epilepsy (e.g., Brugada syndrome 7 due to SCN3B mutation), 12) Genes not listed in Online Mendelian Inheritance in Man (OMIM). Consent forms available on the websites were critically reviewed for their content and extent of detail listed. Content studied included basic information about genetic testing and explanation of tests (description of general genetics and next generation sequencing test process), and possible results (positive, negative and variants of uncertain significance), information about insurance, genetic information nondiscrimination act (GINA), genetic counseling and test limitation.

Results Review of Genes on Panels The NGS panels varied significantly in the number of genes included (70–465 genes). All panels, except GeneDx, included genes not known to be associated with primary epilepsy (1–4 % of panel contents), including neural tube defects, certain channelopathies causing prolonged QT interval and other arrhythmias (e.g., SCN3B mutation), and other genetic syndromes that do not include primary epilepsy (e.g., optic atrophy 1, OPA1 mutation). The panels also included genes for lysosomal storage disorders (6–12 %), congenital disorders of glycosylation (0–8.5 %), disorders of peroxisomal biogenesis (0–3 %) and rare metabolic and mitochondrial disorders (3.5–34 %). Neurological syndromes (18–43 %) and other known genetic syndromes (6.4–21 %) were also included. Specific details of each panel are shown in the pie charts in Fig. 1. We compared the different laboratories to Courtagen as it is the largest epilepsy panel we studied. Specific details are shown in Fig. 2. Coverage of all other laboratories was between 80 and 99.3 % of Courtagen panel genes, with the lowest being Medical Neurogenetics (Fig. 2). Twenty-three percent of genes on Medical Neurogenetics panel were not on any other panel as shown in Fig. 3. Approximately 15 % of genes on the Courtagen epilepsy panel were not on any other panels. Genetic/ Dysmorphology syndromes and neurological syndromes are listed in Table 1 and the corresponding genes are provided in Supplemental File.

Review of Consent Forms American College of Medical Genetics (ACMG) recommends informed consent documentation, and pretest counselling including discussion of testing outcomes but physician practices vary widely (Green et al. 2013). This is reflected by the diverse consent practices used by the various laboratories. Greenwood Genetics and Medical Neurogenetics did not have consent forms available on their website. Informed consents differed significantly between laboratories ranging from basic information about genetic testing and possible results (positive, negative and variants of uncertain significance) to information about insurance, genetic information nondiscrimination act (GINA), genetic counseling and test limitation. All laboratories have a cost associated with doing parental testing when there is a known mutation identified. If a VUS is identified, all labs except for Medical Neurogenetics will offer parental studies free of charge, in most cases (case by case in case of more than two variants). Comparison of the epilepsy panel consent forms is listed in Table 2.

Review of commercially available epilepsy genetic panels

Fig. 1 Distribution of the phenotypes included in each panel

Discussion Our findings suggest that it is important to consider the range of genes offered on epilepsy panels and their predicted phenotypes in an effort toward improving the informed consent process. Pretest counseling is very important and here we discuss several issues that are unique to epilepsy panels.

Fig. 2 Coverage of all laboratories compared to Courtagen panel

1) Our careful review of all genes showed that in some panels, genes not currently associated with epilepsy were included (up to 4 % of panel content). Some of these genes were for potentially life-threatening conditions like Brugada syndrome 7 due to SCN3B mutation. A patient presenting with recurrent syncopal episodes due to Brugada syndrome might be mistakenly diagnosed as intractable epilepsy (recurrent syncopal episodes could be considered Bdrop seizures^ if they are unwitnessed). Some channelopathies causing arrhythmias have also been linked to seizures like SCN5A (Parisi et al. 2013). We classified these genes in the category Bprobable linked to epilepsy^. Hence the panels that include genes for prolonged QT syndrome might be appropriate in such settings to provide a definite diagnosis for the family. Thus, the possibility of identifying a variant in one of these genes must be discussed as this can have implications for the entire family. One could argue that such large panels will lead to novel phenotype discoveries linked to the same gene, however this needs to included in the discussion during pretest counseling. A review of mitochondrial disease panels was previously conducted and similar conclusions were drawn (Platt et al. 2014). 2) Having more genes on the panel is not always ideal especially when the phenotype of the patient is well defined.

Chambers, Jansen and Dhamija Fig. 3 Percentage of genes that are unique to a panel

Sequencing more genes brings a higher likelihood of identifying variants of unknown significance in genes that are not related to a patient’s phenotype, creating confusion for both clinicians and families. Laboratories should specify in the reporting if parental testing at no-charge is offered to help clarify these variants. Since the larger epilepsy panels include genes for lysosomal storage diseases, pharmacogenomics, peroxisomal disorders and mitochondrial disorders, families should be informed of the possibility of finding carrier status as well as potential neurodegenerative disorders that may not manifest until later in life. 3) These panels could also lead to diagnosis of disorders that have multisystemic manifestations. Several of these syndromes are listed in Table 1. One could argue that syndromes like Neurofibromatosis type 1 and Tuberos Sclerosis, that have every distinct physical manifestation, should not be on a large panel testing for epilepsy as we Table 1

might find variants of uncertain significance in these genes in individuals who do not meet the clinical criteria, adding to the interpretative uncertainty. On the other hand there are clear advantages of diagnosing a genetic disorder with systemic features early, for example in syndromes like Neurofibromatosis type 1 and Tuberos Sclerosis, surveillance programs can be started soon after diagnosis. Physicians should be prepared to make individual decisions with regards to type of panel selection based on their clinical assessment. 4) Some of the larger panels include recently discovered genes or genes with variable expressivity and have helped expand the phenotypes associated with mutations in such genes. Larger and more comprehensive panels may be indicated when phenotype is not specific and family history is very suggestive of a genetic etiology. Larger panels have enabled molecular diagnosis of atypical phenotypes

List of Genetic and Neurologic syndromes included in the panels

Genetic/Dysmorphology Syndromes

Neurological Syndromes

Menkes disease, Alpha-thalassemia, X-linked Intellectual disability, Neurofibromatosis type 1, Cardio-facio-cutaneous syndrome, Noonan syndrome-like disorder, LEOPARD syndrome, Costello syndrome, Legius syndrome, Pitt hopkins like syndrome, Orofaciodigital syndrome, Cornelia de lange syndrome, Knobloch syndrome, Lujanfryns syndrome, Brain small vessel disease with Axenfeld-rieger anomaly and porencephaly, Crouzon syndrome with acanthosis nigricans, Muenke syndrome, Thanatophoric dysplasia, Dubowitz syndrome, oculodentodigital dysplasia, Greig cephalopolysyndactyly syndrome, Simpson-golabi-behmel syndrome Neonatal diabetes mellitus, Goldberg-shprintzen syndrome, Kabuki syndrome, Microcephalic osteodysplastic primordial dwarfism, Borjesonforssman-lehmann syndrome, Smith magenis syndrome, Schinzelgiedion midface retraction syndrome, Wolfram syndrome, Cohen syndrome, Velocardiofacial syndrome, Tuberous sclerosis complex, Angelman syndrome

Joubert syndrome, Megalencephaly-polymicrogyria-polydactlyhydrocephalous syndrome, Megalencephaly-capillary-malformationpolymicrogyria syndrome, Ataxia, early-onset with oculomotor apraxia and hypoalbuminemia, Periventricular heterotopia with microcephaly, autosomal recessive microcephaly, Dentatorubro-pallidoluysian atrophy, Alternating hemiplegia of childhood, familial hemiplegic migraine, Autosomal dominant and X linked intellectual disability, Holoprosencephaly, Lissencephaly, Subcortical laminal heteropia, Schizencephaly, Perventricular heterotopia, AlphaDystroglycanopathies, Genetic forms of leukoencephalopathy, Pelizaeus-merzbacher disease, Megalencephalic leukoencephalopathy with subcortical cysts, Aicardi-goutieres syndrome, Rett syndrome, Alexander disease, Hereditary hyperekplexia, Neurodegeneration with brain iron accumulation, pontocerebellar hypoplasia, Episodic ataxia, Choreoacanthocytosis, Mowat-wilson syndrome

LEOPARD syndrome: acronym for multiple lentigines, electrocardiographic abnormalities, ocular hypertelorism, pulmonary stenosis, abnormal genitalia, retardation of growth and sensorineural deafness

Review of commercially available epilepsy genetic panels Table 2

Comparison of the epilepsy panel consent forms

Laboratory Consent Forms

Explanation of tests

Possible Results (positive, negative, variant) X

X

GeneDx

X

X

X

X

Courtagen Transgenomics

X

X X

X

X

X X

X X

Athena Diagnostics

X

X

X

X

X

X

Emory Genetics

Limitations of testing

Confidentiality and releasing results

GINA

Free parental testing if a VUS is identified X X

**Greenwood Genetics and Medical Neurogenetics did not have consent forms available on their website **All labs have a cost associated with doing parental testing when there is a known mutation identified. If a VUS is identified, all labs except for Medical Neurogenetics will offer parental studies free of charge, in most cases

and have enabled clinicians to link phenotype with novel genes, hence leading to gene discoveries.

Funding None.

References Conclusions Genetic Counselors are in a good position to help with the selection of epilepsy panels. Clinicians who care for epilepsy patients should clearly communicate to families the range of disorders included in the panels. Pretest counseling is of utmost importance to discuss all issues including yield of testing, limitation of testing, possible results, interpretive uncertainty in some cases and its implications for the patients and family members (Ormond 2013). Some of these are unique issues to epilepsy panels (as discussed in detail above) while others are similar to those encountered in any next generation panel testing. We can safey conclude that there is not a single best epilepsy NGS panel and that at this time the panel should be selected based on each patient’s presentation while respecting patients and/or parents wishes. Commercial laboratories need to work towards improving the informed consent process so that patients are aware of exactly what testing they are receiving and its full implications. Consent forms should be easily accessible online along with epilepsy panel information and informed consent process should be made more standardized and perhaps mandatory in the era of evolving genomics. Compliance with ethical standards Author Contributions Chelsea Chambers and Radhika Dhamija wrote the first draft of the manuscript. Radhika Dhamija and Laura Jansen provided critical review and supervision. Declaration of Conflicting Interests All authors have no conflicts of interest to declare

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