Pitfalls in genetic testing: the story of missed SCN1A mutations

BACKGROUND: Sanger sequencing, still the standard technique for genetic testing in most diagnostic laboratories and until recently widely used in research, is gradually being complemented by next-generation sequencing (NGS). No single mutation detection technique is however perfect in identifying all mutations. Therefore, we wondered to what extent inconsistencies between Sanger sequencing and NGS affect the molecular diagnosis of patients. Since mutations in SCN1A, the major gene implicated in epilepsy, are found in the majority of Dravet syndrome (DS) patients, we focused on missed SCN1A mutations. METHODS: We sent out a survey to 16 genetic centers performing SCN1A testing. RESULTS: We collected data on 28 mutations initially missed using Sanger sequencing. All patients were falsely reported as SCN1A mutation-negative, both due to technical limitations and human errors. CONCLUSION: We illustrate the pitfalls of Sanger sequencing and most importantly provide evidence that SCN1A mutations are an even more frequent cause of DS than already anticipated

Prevalence and onset of comorbidities in the CDKL5 disorder differ from Rett syndrome

Background: Initially described as an early onset seizure variant of Rett syndrome, the CDKL5 disorder is now considered as an independent entity. However, little is currently known about the full spectrum of comorbidities that affect these patients and available literature is limited to small case series. This study aimed to use a large international sample to examine the prevalence in this disorder of comorbidities of epilepsy, gastrointestinal problems including feeding difficulties, sleep and respiratory problems and scoliosis and their relationships with age and genotype. Prevalence and onset were also compared with those occurring in Rett syndrome. Methods: Data for the CDKL5 disorder and Rett syndrome were sourced from the International CDKL5 Disorder Database (ICDD), InterRett and the Australian Rett syndrome Database (ARSD). Logistic regression (multivariate and univariate) was used to analyse the relationships between age group, mutation type and the prevalence of various comorbidities. Binary longitudinal data from the ARSD and the equivalent cross-sectional data from ICDD were examined using generalized linear models with generalized estimating equations. The Kaplan-Meier method was used to estimate the failure function for the two disorders and the log-rank test was used to compare the two functions. Results: The likelihood of experiencing epilepsy, GI problems, respiratory problems, and scoliosis in the CDKL5 disorder increased with age and males were more vulnerable to respiratory and sleep problems than females. We did not identify any statistically significant relationships between mutation group and prevalence of comorbidities. Epilepsy, GI problems and sleep abnormalities were more common in the CDKL5 disorder than in Rett syndrome whilst scoliosis and respiratory problems were less prevalent. Conclusion: This study captured a much clearer picture of the CDKL5 disorder than previously possible using the largest sample available to date. There were differences in the presentation of clinical features occurring in the CDKL5 disorder and in Rett syndrome, reinforcing the concept that CDKL5 is an independent disorder with its own distinctive characteristics

Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data

The classic epileptic encephalopathies, including infantile spasms (IS) and Lennox–Gastaut syndrome (LGS), are severe seizure disorders that usually arise sporadically. De novo variants in genes mainly encoding ion channel and synaptic proteins have been found to account for over 15% of patients with IS or LGS. The contribution of autosomal recessive genetic variation, however, is less well understood. We implemented a rare variant transmission disequilibrium test (TDT) to search for autosomal recessive epileptic encephalopathy genes in a cohort of 320 outbred patient–parent trios that were generally prescreened for rare metabolic disorders. In the current sample, our rare variant transmission disequilibrium test did not identify individual genes with significantly distorted transmission over expectation after correcting for the multiple tests. While the rare variant transmission disequilibrium test did not find evidence of a role for individual autosomal recessive genes, our current sample is insufficiently powered to assess the overall role of autosomal recessive genotypes in an outbred epileptic encephalopathy population

A survey on container processing in railway yards: Decision problems, optimization procedures and research challenges

In spite of extraordinary support programs initiated by the European Union and other national authorities, the percentage of overall freight traffic moved by train is in steady decline. This development is driven by the fact that macro-economic benefits of rail traffic, such as relief of overloaded road networks and reduced environmental impacts, are countervailed by severe disadvantages from the perspective of the shipper, e.g., low average delivery speed and general lack of reliability. Attracting a higher share of freight traffic on rail requires a more efficient freight handling in railway yards, which includes technical innovations as well as the development of suited decision support systems. This paper reviews container processing in railway yards from an operational research perspective and analyzes basic decision problems for the two most important yard types, namely conventional rail-road and modern rail-rail transshipment yards. Existing literature is reviewed and open research challenges are identified.Railway System, Railway Yard, Container Processing, Decision Support, Survey

Hilfen fuer Hoergeschaedigte. Erstellung von Kriterien zur Bewertung, Optimierung und Entwicklung von Cochleaimplantanten anhand neuronaler Antworten im auditorischen Mittelhirn auf elektrische Stimulation des Hoernerven Abschlussbericht

The present report discusses animal experiments investigating the coding of temporal signal parameters in the auditory system from single channel cochlear implants. The significance of the question arises out of the fact that temporal information - in opposition to frequency information that in normal hearing is coded in the cochlea by complex vibrations - can be easily transmitted by electrical stimulation. The starting point of the investigations was research results showing that the central auditory system, in addition to a frequency analysis in the periphery, carries out a temporal analysis of acoustic signals. To obtain a comparative overview of responses to acoustic and electrical stimuli in the auditory system of our experimental subjects (Chinchilla laniger), the 14C-2-Deoxyglucose and c-fos immunohistochemical methods were used. After stimulation with either periodic acoustic or electrical stimuli, both methods demonstrated spatially patterned markings in auditory midbrain (IC). These are caused by activations of cell arrays that run from dorsal to ventral, and whose position shifts with periodicity. These results confirm and support previous findings of ours, until now only arising from reconstructions of electrophysiological data, showing activation patterns from periodic signals orthogonal to the isofrequency contours. Further investigations were made to see if electrical stimulation via a single electrode at the round window would produce the same temporal activity pattern as an acoustic stimulus. For this, the responses of cells in IC to acoustic pulses, sinusoidal and amplitude modulated signals were measured and compared to the responses from electrical stimuli applied to the round window. The results show that the temporal neural response parameters from electrical and acoustic signals are similar to a great extent in many cases. In particular, neurons were found whose modulation transfer functions were only minimally different. This is an important point for the application of cochlear implants, since low frequency (1-20 Hz) and high frequency (20-1000 Hz) modulations play an important role in speech processing. The observed differences in temporal response parameters of neurons to acoustic and electrical signals, could be minimised by variations in coding of the electrical signal. These investigations show that the spatial and temporal response parameters in the auditory midbrain are appropriate criteria to test suitability of coding strategies for cochlear implants in an animal model. (orig.)SIGLEAvailable from TIB Hannover: F97B1450 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekBundesministerium fuer Bildung, Wissenschaft, Forschung und Technologie, Bonn (Germany)DEGerman

Integrating ship movement scheduling and tug assignment within a canal harbor

In this paper we address the in-port ship scheduling and tug assignment problem. This problem aims to determine a schedule of ship movements, and their escorting tugs, within a canal harbor. We formulate the problem as a Boolean satisfiability problem. In particular, we deal with canal-harbors, as this kind of harbors present strict constraints, e.g., on safety distance. We consider the Port of Venice, a medium size Italian harbor, as a case stud