Simon Glynn

De novo mutations in epileptic encephalopathies

Epileptic encephalopathies are a devastating group of severe childhood epilepsy disorders for which the cause is often unknown. Here we report a screen for de novo mutations in patients with two classical epileptic encephalopathies: infantile spasms (n = 149) and Lennox–Gastaut syndrome (n = 115). We sequenced the exomes of 264 probands, and their parents, and confirmed 329 de novo mutations. A likelihood analysis showed a significant excess of de novo mutations in the ∼4,000 genes that are the most intolerant to functional genetic variation in the human population (P = 2.9 × 10−3). Among these are GABRB3, with de novo mutations in four patients, and ALG13, with the same de novo mutation in two patients; both genes show clear statistical evidence of association with epileptic encephalopathy. Given the relevant site-specific mutation rates, the probabilities of these outcomes occurring by chance are P = 4.1 × 10−10 and P = 7.8 × 10−12, respectively. Other genes with de novo mutations in this cohort include CACNA1A, CHD2, FLNA, GABRA1, GRIN1, GRIN2B, HNRNPU, IQSEC2, MTOR and NEDD4L. Finally, we show that the de novo mutations observed are enriched in specific gene sets including genes regulated by the fragile X protein (P < 10−8), as has been reported previously for autism spectrum disorders.

A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T

This paper describes the construction of a computational anatomical atlas of the human hippocampus. The atlas is derived from high-resolution 9.4 Tesla MRI of postmortem samples. The main subfields of the hippocampus (cornu ammonis fields CA1, CA2/3; the dentate gyrus; and the vestigial hippocampal sulcus) are labeled in the images manually using a combination of distinguishable image features and geometrical features. A synthetic average image is derived from the MRI of the samples using shape and intensity averaging in the diffeomorphic non-linear registration framework, and a consensus labeling of the template is generated. The agreement of the consensus labeling with manual labeling of each sample is measured, and the effect of aiding registration with landmarks and manually generated mask images is evaluated. The atlas is provided as an online resource with the aim of supporting subfield segmentation in emerging hippocampus imaging and image analysis techniques. An example application examining subfield-level hippocampal atrophy in temporal lobe epilepsy demonstrates the application of the atlas to in vivo studies.

Ultra-rare genetic variation in common epilepsies: a case-control sequencing study

BACKGROUND Despite progress in understanding the genetics of rare epilepsies, the more common epilepsies have proven less amenable to traditional gene-discovery analyses. We aimed to assess the contribution of ultra-rare genetic variation to common epilepsies. METHODS We did a case-control sequencing study with exome sequence data from unrelated individuals clinically evaluated for one of the two most common epilepsy syndromes: familial genetic generalised epilepsy, or familial or sporadic non-acquired focal epilepsy. Individuals of any age were recruited between Nov 26, 2007, and Aug 2, 2013, through the multicentre Epilepsy Phenome/Genome Project and Epi4K collaborations, and samples were sequenced at the Institute for Genomic Medicine (New York, USA) between Feb 6, 2013, and Aug 18, 2015. To identify epilepsy risk signals, we tested all protein-coding genes for an excess of ultra-rare genetic variation among the cases, compared with control samples with no known epilepsy or epilepsy comorbidity sequenced through unrelated studies. FINDINGS We separately compared the sequence data from 640 individuals with familial genetic generalised epilepsy and 525 individuals with familial non-acquired focal epilepsy to the same group of 3877 controls, and found significantly higher rates of ultra-rare deleterious variation in genes established as causative for dominant epilepsy disorders (familial genetic generalised epilepsy: odd ratio [OR] 2·3, 95% CI 1·7-3·2, p=9·1 × 10-8; familial non-acquired focal epilepsy 3·6, 2·7-4·9, p=1·1 × 10-17). Comparison of an additional cohort of 662 individuals with sporadic non-acquired focal epilepsy to controls did not identify study-wide significant signals. For the individuals with familial non-acquired focal epilepsy, we found that five known epilepsy genes ranked as the top five genes enriched for ultra-rare deleterious variation. After accounting for the control carrier rate, we estimate that these five genes contribute to the risk of epilepsy in approximately 8% of individuals with familial non-acquired focal epilepsy. Our analyses showed that no individual gene was significantly associated with familial genetic generalised epilepsy; however, known epilepsy genes had lower p values relative to the rest of the protein-coding genes (p=5·8 × 10-8) that were lower than expected from a random sampling of genes. INTERPRETATION We identified excess ultra-rare variation in known epilepsy genes, which establishes a clear connection between the genetics of common and rare, severe epilepsies, and shows that the variants responsible for epilepsy risk are exceptionally rare in the general population. Our results suggest that the emerging paradigm of targeting of treatments to the genetic cause in rare devastating epilepsies might also extend to a proportion of common epilepsies. These findings might allow clinicians to broadly explain the cause of these syndromes to patients, and lay the foundation for possible precision treatments in the future. FUNDING National Institute of Neurological Disorders and Stroke (NINDS), and Epilepsy Research UK.

Appearance and incomplete label matching for diffeomorphic template based hippocampus segmentation

We present a robust, high‐throughput, semiautomated template‐based protocol for segmenting the hippocampus in temporal lobe epilepsy. The semiautomated component of this approach, which minimizes user effort while maximizing the benefit of human input to the algorithm, relies on “incomplete labeling.” Incomplete labeling requires the user to quickly and approximately segment a few key regions of the hippocampus through a user‐interface. Subsequently, this partial labeling of the hippocampus is combined with image similarity terms to guide volumetric diffeomorphic normalization between an individual brain and an unbiased disease‐specific template, with fully labeled hippocampi. We solve this many‐to‐few and few‐to‐many matching problem, and gain robustness to inter and intrarater variability and small errors in user labeling, by embedding the template‐based normalization within a probabilistic framework that examines both label geometry and appearance data at each label. We evaluate the reliability of this framework with respect to manual labeling and show that it increases minimum performance levels relative to fully automated approaches and provides high inter‐rater reliability. Thus, this approach does not require expert neuroanatomical training and is viable for high‐throughput studies of both the normal and the highly atrophic hippocampus.

Acute intermittent porphyria presenting as a diffuse encephalopathy.

Although acute intermittent porphyria presents with dramatic neurological findings, the diagnosis is difficult. An 18‐year‐old woman had a clinical picture of porphyric encephalopathy. Magnetic resonance (MR) imaging demonstrated multiple large contrast‐enhancing subcortical white matter lesions, which regressed with glucose and hematin infusions. Diffusion‐weighted MR imaging was normal, and MR spectroscopy excluded acute demyelination or tissue necrosis. MR findings of acute intermittent porphyria can differ from those in posterior reversible encephalopathy syndrome by virtue of intense contrast enhancement. Because diffusion‐weighted MR imaging and spectroscopy were normal, the lesions are likely caused by reversible vasogenic edema and transient breakdown of the blood–brain barrier. Ann Neurol 2005;57:581–584

Hippocampal volumetry and functional MRI of memory in temporal lobe epilepsy.

This study examined the utility of structural and functional MRI at 1.5 and 3T in the presurgical evaluation and prediction of postsurgical cognitive outcome in temporal lobe epilepsy (TLE). Forty-nine patients undergoing presurgical evaluation for temporal lobe (TL) resection and 25 control subjects were studied. Patients completed standard presurgical evaluations, including the intracarotid amobarbital test (IAT) and neuropsychological testing. During functional imaging, subjects performed a complex visual scene-encoding task. High-resolution structural MRI scans were used to quantify hippocampal volumes. Both structural and functional imaging successfully lateralized the seizure focus and correlated with IAT memory lateralization, with improvement for functional imaging at 3T as compared with 1.5 T. Ipsilateral structural and functional MRI data were related to cognitive outcome, and greater functional asymmetry was related to earlier age at onset. These findings support continued investigation of the utility of MRI and fMRI in the presurgical evaluation of TLE.

Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy

Infantile spasms (IS) and Lennox–Gastaut syndrome (LGS) are epileptic encephalopathies characterized by early onset, intractable seizures, and poor developmental outcomes. De novo sequence mutations and copy number variants (CNVs) are causative in a subset of cases. We used exome sequence data in 349 trios with IS or LGS to identify putative de novo CNVs. We confirm 18 de novo CNVs in 17 patients (4.8%), 10 of which are likely pathogenic, giving a firm genetic diagnosis for 2.9% of patients. Confirmation of exome‐predicted CNVs by array‐based methods is still required due to false‐positive rates of prediction algorithms. Our exome‐based results are consistent with recent array‐based studies in similar cohorts and highlight novel candidate genes for IS and LGS. Ann Neurol 2015;78:323–328

Potential for unreliable interpretation of EEG recorded with microelectrodes

Recent studies in epilepsy, cognition, and brain machine interfaces have shown the utility of recording intracranial electroencephalography (iEEG) with greater spatial resolution. Many of these studies utilize microelectrodes connected to specialized amplifiers that are optimized for such recordings. We recently measured the impedances of several commercial microelectrodes and demonstrated that they will distort iEEG signals if connected to clinical EEG amplifiers commonly used in most centers. In this study we demonstrate the clinical implications of this effect and identify some of the potential difficulties in using microelectrodes.

One center's experience with complications during the Wada test

This study aimed to define the number and type of complications associated with the Wada test at an academic medical center for comparison to previous reports. We performed a retrospective review of medical records for patients who underwent the Wada test at the University of Michigan between April 1991 and June 2013. Information was collected regarding the angiography procedure and the immediate postoperative period to assess for both clinical and angiographic complications. A total of 436 patients were identified who underwent the Wada procedure between April 1991 and June 2013, and 431 patients were included in the final analysis. Twenty‐five patients (5.8%) had notable clinical events associated with the Wada test. Nine patients (2.1%) had clinical events meeting criteria for complication, which included seizures, status epilepticus, internal carotid artery vasospasm, inadvertent injection of anesthetic in the external carotid artery, and transient encephalopathy. No complications were associated with significant morbidity or mortality. This retrospective review of patients undergoing the Wada test found significantly fewer associated complications in comparison to previously published studies, with no patients experiencing long‐term morbidity. The Wada test should be considered a safe diagnostic tool for lateralizing language and memory.

A High-Resolution Computational Atlas of the Human Hippocampus from Postmortem Magnetic Resonance Imaging at 9.4 Tesla

This paper describes the construction of a computational anatomical atlas of the human hippocampus. The atlas is derived from high-resolution 9.4 Tesla MRI of postmortem samples. The main subfields of the hippocampus (cornu Ammonis fields CA1, CA2/3; the dentate gyrus; and the vestigial hippocampal sulcus) are labeled in the images manually using a combination of distinguishable image features and geometrical features. A synthetic average image is derived from the MRI of the samples using shape and intensity averaging in the diffeomorphic non-linear registration framework, and a consensus labeling of the template is generated. The agreement of the consensus labeling with manual labeling of each sample is measured, and the effect of aiding registration with landmarks and manually generated mask images is evaluated. The atlas is provided as an online resource with the aim of supporting subfield segmentation in emerging hippocampus imaging and image analysis techniques. An example application examining subfield-level hippocampal atrophy in temporal lobe epilepsy demonstrates the application of the atlas to in vivo studies.