The utility of exome sequencing for genetic diagnosis in a familial microcephaly epilepsy syndrome

Although up to 70% of patients with epilepsy have an underlying genetic cause [1], most patients with epilepsy will not receive a molecular diagnosis. Genetic testing for epilepsies is challenging since genetic heterogeneity for this group of conditions is significant. For instance, epilepsy can be caused by mutations in over 260 genes and an accurate diagnosis can be particularly difficult with nonspecific epilepsy phenotypes [2]. Even when epilepsy is associated with additional features, such as microcephaly, the number of genes potentially responsible can still be significant and assessing each gene in turn by Sanger sequencing would be time-consuming and expensive. However, establishing a molecular diagnosis is important for informed genetic counseling, prenatal testing, insight into natural history and increasingly for therapeutic management as there are now many instances where medications are tailored based on molecular results [3‐5].

Whole exome sequencing (WES) has emerged as a very successful tool for novel disease gene discovery [6] and its utility in the rapid and cost-effective analysis of heterogeneous disorders is being established. Both a WES approach and the application of targeted panels of channelopathy or encephalopathy genes have been successful in identifying the molecular cause for many patients with rare epilepsies [2, 7]. In addition, WES may offer a rapid and less expensive first line test to establish a molecular diagnosis for disabled patients residing in remote areas where ready access to standard diagnostic assessments can be more challenging. We report here the utility of WES as the initial diagnostic tool for a consanguineous family with four affected adult children with epilepsy, microcephaly and severe intellectual disability from a remote area of Canada.

Primary autosomal recessive microcephaly (MCPH, OMIM 251200) is a genetically heterogeneous group of disorders characterized by congenital microcephaly, cognitive impairment and variable epilepsy [12]. Mutations in WDR62 are associated with primary microcephaly-2 (MCPH2, OMIM 604317), which is believed to account for 10% of all cases of MCPH [13]. Clinical features of MCPH2 include epilepsy, marked cognitive impairment, incontinence, sloping forehead and prominent ears. Radiological features are variable and may include polymicrogyria, corpus callosum hypoplasia, heterotopias, pachygyria with cortical thickening, lissencephaly and schizencephaly, although patients can present with isolated microcephaly [14‐18]. To date, 34 families have been identified with mutations in WDR62, the reported affected individuals ranging in age from infancy to mid-teens [14‐18].We present here the oldest patients known to have WDR62 mutations associated with MCPH, providing additional insight into the natural history and phenotypic spectrum of this disorder. It is unclear whether the sudden cardiac death for Patient II-2 is associated with WDR62 mutations or an unrelated cardiac event. Of the mutations in WDR62 reported thus far, approximately half have been frameshift mutations, as described here, distributed throughout the gene and predicted to result in premature truncation of the protein (Figure 1C).

At least ten genes have been associated with MCPH [ASPM, MCPH1, WDR62, CDK5RAP2, CASC5, CENPJ, STIL, CEP135, CEP152 and ZNF335] and are implicated in proliferation and migration of neuronal progenitors during embryonic cortical development [19]. Clinical-radiological features have not been loci-specific and MCPH patients remain phenotypically indistinguishable [13]. Thus, conventional molecular testing can be a long and expensive process and may not yield a diagnosis. Currently, sequential analysis of the eight clinically available MCPH genes would total more than $22,000 USD. Alternatively, eight of the ten MCPH genes could be sequenced as part of a microcephaly panel for $7,000 USD (http://​www.​centogene.​com accessed November 6^th, 2013, eight genes). Comparatively, WES would interrogate all ten microcephaly genes and is currently available in clinical laboratories at $5000 USD per patient, making it a cost-effective solution for rapid diagnosis in the clinic.

We studied four siblings from a consanguineous French Canadian family presenting with microcephaly, severe developmental delay and epilepsy. Given their relatively nonspecific phenotype which did not suggest a single likely candidate gene, sequential gene testing was not undertaken. Alternatively, WES provided a cost-effective and rapid method to identify the genetic cause of epilepsy and microcephaly in this family. We highlight, that particularly for patients in remote areas, WES via DNA blood/saliva offers a non-invasive and readily accessible method for shortening the diagnostic process for these patients.