Epilepsy and developmental disorders: Next generation sequencing in the clinic

Background: The advent of Next Generation Sequencing (NGS) has led to a redefining of the genetic landscape of the epilepsies. Hundreds of single gene epilepsies have been described. Genes associated with epilepsy involve diverse processes. Now a substantial proportion of individuals with epilepsy can receive a high definition molecular genetic diagnosis. / Methods: In this review we update the current genetic landscape of the epilepsies and categorise the major functional groupings of epilepsy-associated genes. We describe currently available genetic testing approaches. We perform a literature review of NGS studies and review the factors which determine yield in cohorts undergoing testing. We identify factors associated with positive genetic diagnosis and consider the utility of genetic testing in terms of treatment selection as well as more qualitative aspects of care. / Findings: Epilepsy-associated genes can be grouped into five broad functional categories: ion transport; cell growth and differentiation; regulation of synaptic processes; transport and metabolism of small molecules within and between cells; and regulation of gene transcription and translation. Early onset of seizures, drug-resistance, and developmental comorbidity are associated with higher diagnostic yield. The most commonly implicated genes in NGS studies to date, in order, are SCN1A, KCNQ2, CDKL5, SCN2A, and STXBP1. In unselected infantile cohorts PRRT2, a gene associated with self-limited epilepsy, is frequently implicated. Genetic diagnosis provides utility in terms of treatment choice closing the diagnostic odyssey, avoiding unnecessary further testing, and informing future reproductive decisions. / Conclusions: Genetic testing has become a first line test in epilepsy. As techniques improve and understanding advances, its utility is set to increase. Genetic diagnosis, particularly in early onset developmental and epileptic encephalopathies, influences treatment choice in a significant proportion of patients. The realistic prospect of gene therapy is a cause for optimism

SCN1A variants from bench to bedside-improved clinical prediction from functional characterization

Variants in the SCN1A gene are associated with a wide range of disorders including genetic epilepsy with febrile seizures plus (GEFS+), familial hemiplegic migraine (FHM), and the severe childhood epilepsy Dravet syndrome (DS). Predicting disease outcomes based on variant type remains challenging. Despite thousands of SCN1A variants being reported, only a minority has been functionally assessed. We review the functional SCN1A work performed to date, critically appraise electrophysiological measurements, compare this to in silico predictions, and relate our findings to the clinical phenotype. Our results show, regardless of the underlying phenotype, that conventional in silico software correctly predicted benign from pathogenic variants in nearly 90%, however was unable to differentiate within the disease spectrum (DS vs. GEFS+ vs. FHM). In contrast, patch‐clamp data from mammalian expression systems revealed functional differences among missense variants allowing discrimination between disease severities. Those presenting with milder phenotypes retained a degree of channel function measured as residual whole‐cell current, whereas those without any whole‐cell current were often associated with DS (p = .024). These findings demonstrate that electrophysiological data from mammalian expression systems can serve as useful disease biomarker when evaluating SCN1A variants, particularly in view of new and emerging treatment options in DS

Prediction of melanoma metastasis by the Shields index based on lymphatic vessel density

<p>Abstract</p> <p>Background</p> <p>Melanoma usually presents as an initial skin lesion without evidence of metastasis. A significant proportion of patients develop subsequent local, regional or distant metastasis, sometimes many years after the initial lesion was removed. The current most effective staging method to identify early regional metastasis is sentinel lymph node biopsy (SLNB), which is invasive, not without morbidity and, while improving staging, may not improve overall survival. Lymphatic density, Breslow's thickness and the presence or absence of lymphatic invasion combined has been proposed to be a prognostic index of metastasis, by Shields et al in a patient group.</p> <p>Methods</p> <p>Here we undertook a retrospective analysis of 102 malignant melanomas from patients with more than five years follow-up to evaluate the Shields' index and compare with existing indicators.</p> <p>Results</p> <p>The Shields' index accurately predicted outcome in 90% of patients with metastases and 84% without metastases. For these, the Shields index was more predictive than thickness or lymphatic density. Alternate lymphatic measurement (hot spot analysis) was also effective when combined into the Shields index in a cohort of 24 patients.</p> <p>Conclusions</p> <p>These results show the Shields index, a non-invasive analysis based on immunohistochemistry of lymphatics surrounding primary lesions that can accurately predict outcome, is a simple, useful prognostic tool in malignant melanoma.</p

Brief psychosocial education, not core stabilization, reduced incidence of low back pain: results from the Prevention of Low Back Pain in the Military (POLM) cluster randomized trial

<p>Abstract</p> <p>Background</p> <p>Effective strategies for the primary prevention of low back pain (LBP) remain elusive with few large-scale clinical trials investigating exercise and education approaches. The purpose of this trial was to determine whether core stabilization alone or in combination with psychosocial education prevented incidence of low back pain in comparison to traditional lumbar exercise.</p> <p>Methods</p> <p>The Prevention of Low Back Pain in the Military study was a cluster randomized clinical study with four intervention arms and a two-year follow-up. Participants were recruited from a military training setting from 2007 to 2008. Soldiers in 20 consecutive companies were considered for eligibility (n = 7,616). Of those, 1,741 were ineligible and 1,550 were eligible but refused participation. For the 4,325 Soldiers enrolled with no previous history of LBP average age was 22.0 years (SD = 4.2) and there were 3,082 males (71.3%). Companies were randomly assigned to receive traditional lumbar exercise, traditional lumbar exercise with psychosocial education, core stabilization exercise, or core stabilization with psychosocial education, The psychosocial education session occurred during one session and the exercise programs were done daily for 5 minutes over 12 weeks. The primary outcome for this trial was incidence of low back pain resulting in the seeking of health care.</p> <p>Results</p> <p>There were no adverse events reported. Evaluable patient analysis (4,147/4,325 provided data) indicated no differences in low back incidence resulting in the seeking of health care between those receiving the traditional exercise and core stabilization exercise programs. However, brief psychosocial education prevented low back pain episodes regardless of the assigned exercise approach, resulting in a 3.3% (95% CI: 1.1 to 5.5%) decrease over two years (numbers needed to treat (NNT) = 30.3, 95% CI = 18.2 to 90.9).</p> <p>Conclusions</p> <p>Core stabilization has been advocated as preventative, but offered no such benefit when compared to traditional lumbar exercise in this trial. Instead, a brief psychosocial education program that reduced fear and threat of low back pain decreased incidence of low back pain resulting in the seeking of health care. Since this trial was conducted in a military setting, future studies are necessary to determine if these findings can be translated into civilian populations.</p> <p>Trial Registration</p> <p><a href="http://www.clinicaltrials.gov/ct2/show/NCT00373009">NCT00373009</a> at ClinicalTrials.gov - <url>http://clinicaltrials.gov/</url></p

The Deadly Chytrid Fungus: A Story of an Emerging Pathogen

[Extract] Emerging infectious diseases present a great challenge for the health of both humans and wildlife. The increasing prevalence of drug-resistant fungal pathogens in humans [1] and recent outbreaks of novel fungal pathogens in wildlife populations [2] underscore the need to better understand the origins and mechanisms of fungal pathogenicity. One of the most dramatic examples of fungal impacts on vertebrate populations is the effect of the amphibian disease chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd).\ud Amphibians around the world are experiencing unprecedented population losses and local extinctions [3]. While there are multiple causes of amphibian declines, many catastrophic die-offs are attributed to Bd [4],[5]. The chytrid pathogen has been documented in hundreds of amphibian species, and reports of Bd's impact on additional species and in additional geographic regions are accumulating at an alarming rate (e.g., see http://www.spatialepidemiology.net/bd). Bd is a microbial, aquatic fungus with distinct life stages. The motile stage, called a zoospore, swims using a flagellum and initiates the colonization of frog skin. Within the host epidermal cells, a zoospore forms a spherical thallus, which matures and produces new zoospores by dividing asexually, renewing the cycle of infection when zoospores are released to the skin surface (Figure 1). Bd is considered an emerging pathogen, discovered and described only a decade ago [6],[7]. Despite intensive ecological study of Bd over the last decade, a number of unanswered questions remain. Here we summarize what has been recently learned about this lethal pathogen

Predictors of Occurrence and Severity of First Time Low Back Pain Episodes: Findings from a Military Inception Cohort

Primary prevention studies suggest that additional research on identifying risk factors predictive of low back pain (LBP) is necessary before additional interventions can be developed. In the current study we assembled a large military cohort that was initially free of LBP and followed over 2 years. The purposes of this study were to identify baseline variables from demographic, socioeconomic, general health, and psychological domains that were predictive of a) occurrence; b) time; and c) severity for first episode of self-reported LBP. Baseline and outcome measures were collected via web-based surveillance system or phone to capture monthly information over 2 years. The assembled cohort consisted of 1230 Soldiers who provided self-report data with 518 (42.1%) reporting at least one episode of LBP over 2 years. Multivariate logistic regression analysis indicated that gender, active duty status, mental and physical health scores were significant predictors of LBP. Cox regression revealed that the time to first episode of LBP was significantly shorter for Soldiers that were female, active duty, reported previous injury, and had increased BMI. Multivariate linear regression analysis investigated severity of the first episode by identifying baseline predictors of pain intensity, disability, and psychological distress. Education level and physical fitness were consistent predictors of pain intensity, while gender, smoking status, and previous injury status were predictors of disability. Gender, smoking status, physical health scores, and beliefs of back pain were consistent predictors of psychological distress. These results provide additional data to confirm the multi-factorial nature of LBP and suggest future preventative interventions focus on multi-modal approaches that target modifiable risk factors specific to the population of interest

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV

The performance of muon reconstruction, identification, and triggering in CMS has been studied using 40 inverse picobarns of data collected in pp collisions at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection criteria covering a wide range of physics analysis needs have been examined. For all considered selections, the efficiency to reconstruct and identify a muon with a transverse momentum pT larger than a few GeV is above 95% over the whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4, while the probability to misidentify a hadron as a muon is well below 1%. The efficiency to trigger on single muons with pT above a few GeV is higher than 90% over the full eta range, and typically substantially better. The overall momentum scale is measured to a precision of 0.2% with muons from Z decays. The transverse momentum resolution varies from 1% to 6% depending on pseudorapidity for muons with pT below 100 GeV and, using cosmic rays, it is shown to be better than 10% in the central region up to pT = 1 TeV. Observed distributions of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO

Natural Allelic Variation Defines a Role for ATMYC1: Trichome Cell Fate Determination

The molecular nature of biological variation is not well understood. Indeed, many questions persist regarding the types of molecular changes and the classes of genes that underlie morphological variation within and among species. Here we have taken a candidate gene approach based on previous mapping results to identify the gene and ultimately a polymorphism that underlies a trichome density QTL in Arabidopsis thaliana. Our results show that natural allelic variation in the transcription factor ATMYC1 alters trichome density in A. thaliana; this is the first reported function for ATMYC1. Using site-directed mutagenesis and yeast two-hybrid experiments, we demonstrate that a single amino acid replacement in ATMYC1, discovered in four ecotypes, eliminates known protein–protein interactions in the trichome initiation pathway. Additionally, in a broad screen for molecular variation at ATMYC1, including 72 A. thaliana ecotypes, a high-frequency block of variation was detected that results in >10% amino acid replacement within one of the eight exons of the gene. This sequence variation harbors a strong signal of divergent selection but has no measurable effect on trichome density. Homologs of ATMYC1 are pleiotropic, however, so this block of variation may be the result of natural selection having acted on another trait, while maintaining the trichome density role of the gene. These results show that ATMYC1 is an important source of variation for epidermal traits in A. thaliana and indicate that the transcription factors that make up the TTG1 genetic pathway generally may be important sources of epidermal variation in plants