Benchmarking whole exome sequencing in the German Network for Personalized Medicine

Introduction Whole Exome Sequencing (WES) has emerged as an efficient tool in clinical cancer diagnostics to broaden the scope from panel-based diagnostics to screening of all genes and enabling robust determination of complex biomarkers in a single analysis. Methods To assess concordance, six formalin-fixed paraffin-embedded (FFPE) tissue specimens and four commercial reference standards were analyzed by WES as matched tumor-normal DNA at 21 NGS centers in Germany, each employing local wet-lab and bioinformatics investigating somatic and germline variants, copy-number alteration (CNA), and different complex biomarkers. Somatic variant calling was performed in 494 diagnostically relevant cancer genes. In addition, all raw data were re-analyzed with a central bioinformatic pipeline to separate wet- and dry-lab variability. Results The mean positive percentage agreement (PPA) of somatic variant calling was 76% and positive predictive value (PPV) 89% compared a consensus list of variants found by at least five centers. Variant filtering was identified as the main cause for divergent variant calls. Adjusting filter criteria and re-analysis increased the PPA to 88% for all and 97% for clinically relevant variants. CNA calls were concordant for 82% of genomic regions. Calls of homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI) status were concordant for 94%, 93%, and 93% respectively. Variability of CNAs and complex biomarkers did not increase considerably using the central pipeline and was hence attributed to wet-lab differences. Conclusion Continuous optimization of bioinformatic workflows and participating in round robin tests are recommend

Vasculitis-like hemorrhagic retinal angiopathy in Wegener’s granulomatosis

Background: Granulomatosis with polyangiitis, also known as Wegener’s granulomatosis, is a chronic systemic inflammatory disease that can also involve the eyes. We report a case of massive retinal and preretinal hemorrhages with perivascular changes as the initial signs in granulomatosis with polyangiitis (Wegener’s granulomatosis). Case presentation: A 39-year-old Caucasian male presented with blurred vision in his right eye, myalgia and arthralgia, recurrent nose bleeds and anosmia. Fundus image of his right eye showed massive retinal hemorrhages and vasculitis-like angiopathy, although no fluorescein extravasation was present in fluorescein angiography. Laboratory investigations revealed an inflammation with increased C-reactive protein, elevated erythrocyte sedimentation rate and neutrophil count. Tests for antineutrophil cytoplasmic antibodies (ANCA) were positive for c-ANCA (cytoplasmatic ANCA) and PR3-ANCA (proteinase 3-ANCA). Renal biopsy demonstrated a focal segmental necrotizing glomerulonephritis. Granulomatosis with polyangiitis (Wegener’s granulomatosis) was diagnosed and a combined systemic therapy of cyclophosphamide and corticosteroids was initiated. During 3 months of follow-up, complete resorption of retinal hemorrhages was seen and general complaints as well as visual acuity improved during therapy. Conclusion: Vasculitis-like retinal changes can occur in Wegener’s granulomatosis. Despite massive retinal and preretinal hemorrhages that cause visual impairment, immunosuppressive therapy can improve ocular symptoms

Modeling and Validation of a Membrane Humidifier for PEM Fuel Cell Systems

In PEM fuel cell applications the humidification of the inflowing air is of significance since the electrical conductivity of the membrane and consequently the stack performance strongly depends on the water loading of the electrolyte. In this context a detailed dynamic simulation model describing a conventional passive membrane humidifier was developed and imple-mented into MATLAB/Simulink at the Institute of Technical Thermodynamics of the German Aerospace Centre (Deutsches Zentrum für Luft- und Raumfahrt e.V., DLR) in Stuttgart. The humidifier model is generally based on a finite volume approach balancing energy and mass flow along the main flow path for both wet and dry fluids. For the description of the heat flux a setting of stirred batch reactors was assumed. The energy transfer between the two flows is accomplished using the humidifier membrane as connecting element and thermal mass. The freely adjustable connection sequence of the single reactors allow furthermore for parallel-, counter- and crossflow configuration. The determination of the water exchange stream is carried out by a separate membrane submodule applying also a finite volume approach. The water concentration and loading difference between the flows and within the membrane define therein the driving force for the water diffusion. The water transfer is directed perpendicular to the main flow path

Characterization of fuel cell behavior at low-pressure operation

Fuel cells may help meet new aircraft to cope with increased electrical demands while mitigating environmental and safety concerns. For an optimized integration of fuel cells into this new application area it is necessary to characterize fuel cells under unusual operation conditions, in particular low-pressure ambient conditions and a wide temperature of operation including -55 °C. This contribution presents investigation of fuel cells under low-pressure operation and the influence of low-pressure on the performance of the cell itself and on the fuel cell system. Especially the reduced supply of oxygen as well as the reduced humidification of the cell has an important influence on performance, related current density distribution of the cell and on fuel cell system operation. At the German Aerospace Center (DLR) several test facilities for low-pressure operation (down to 0.2 bar at the fuel cell outlet) of fuel cells have been built-up. For the investigation of the inherent electrochemical cell behavior a standard small cell with 5 x 5 cm2 and single meander flow field was investigated at various operating pressures in a test facilities were low-pressure operation was realized by evacuating the fuel cell exhaust by pumps. The channel in the flow field was 1 mm wide and has a depth of 1 mm on the cathode side and 0.7 mm on the anode side. The rib width was 1 mm. A significant pressure drop results from the flow field design (single channel with a total length of approx. 1.3 m). Consequently the local operating conditions and the related local current density in the test cell vary significantly. The main advantage of the single meander flow field is that the local gas flows in the cell are well defined. In order to yield a detailed understanding of the problems of low-pressure fuel cell operation and correlate the pressure variation along the flow path with the local performance the current density distribution was measured under the different operating conditions. Of course, a strong dependence of the current density distribution on the operating pressure was observed. The most significant alteration in the current density distribution was observed at a operating pressure of 600 mbar at the cell outlet which corresponds to the saturated water vapor pressure at 80°C (pH20, saturation ≈ 450 mbar). The local variations of the current density distribution as a function of the operating pressure can yield relevant information for the optimization of fuel cells and their components for aircraft applications. To correlate the electrochemical behavior of the cell with the influence of the low-pressure operation on the overall fuel cell system, a portable fuel cell system with 300 W power developed at DLR was tested in a vacuum chamber at reduced pressures. In this case all fuel cell systems components including the air supply system had to operate at reduced pressures down to 200 mbar. The observed changes in performance can be analyzed taking into account the single cell behavior which is representative of the electrochemical processes under low-pressure. From this information, an optimized system design becomes possible and the implications will be discussed in this contribution

Studie: Status PEFC-basierter Fahrzeugantriebe und Fahrzeugkonzepte (FCEV-Studie)

In der Studie wird der aktuelle Stand der PEFC-Entwicklung für PKW-Antrieb bei den wesentlichen Fahrzeugherstellern sowie eine Projektion in die Zukunft behandelt

Fuel cell test facilities for low-pressure operation

Caused by the increasing request of electrical power in modern as well as in future aircrafts fuel cells for on-board generation of the electrical power becomes interesting systems. Possible advantages of fuel cells are a higher electrical efficiency compared to the turbines and the diversification of the electrical power generation (increased reliability). However, the analysis of the feasibility of using fuel cells in these applications demands accurate predictions of fuel cell behaviour at the conditions encountered in the flight scenarios. In particular, a passive fuel cell operating on an aircraft at 12000 meters will need to be able to produce power using air that has a pressure only one-quarter of that at sea level, and withstand temperatures of –55 °C or lower. In order to develop and optimize fuel cells for aircraft applications the components must be tested under in-fly conditions. Therefore, test of systems and stacks, as well as single cells should be performed in the pressure range of interest. The adaptation of a fuel cell system to the conditions at high elevations requires a tremendous effort. In order to design the various subsystems and to select appropriate components it is necessary to first identify the requirements and the operation characteristic of fuel cell systems and stacks. For this reason a test facility for small fuel cells systems under low-pressure conditions was design and realized. A complete home-built PEFC fuel cell system of 300 W was tested down to a pressure of 0.2 bar. The goalof these measurements was to ascertain and validate theoretical evaluations and simulations with real experiments. The fuel cell system was integrated into a vacuum chamber with an internal volume of 2.5 m3 and a minimal possible pressure of 0.1 mbar. The necessary adaptations included a hydrogen safety system for low-pressures and installation of a lock systems with valves to ascertain an adequate air supply. Also modifications of the fuel cell system were necessary for reliable operation like an improved cooling fort he compressor and stack and an improvement of the humifidfier. The controls for the system had to be installed outside of the chamber. With this tes facility the German Aerospace Center (DLR) tested for the first time in Europe a fuel cell system under low-pressure conditions of 0.2 bar (abs.), which corresponds to an altitude of 12000 m. However, in order to consider all relevant aspects for this application also stack and cell design have to be improved for this specific application. In the stack design the pressure drop must be reduced compared to stacks for operation under normal conditions, because the pressure drop significant increases with decreasing operating pressure (Δp∼1/p). The second fundamental problem is the water management in low pressure operation. In order to ensure a good humidification of the cell the water partial pressure in the feed gas should be the saturated water vapor pressure of the cell temperature. However, under flying conditions the saturated water vapor pressure of water can be higher than the total operating pressure; e.g. at 80°C the saturated water vapor pressure is approx. 45000 Pa (450 mbar). Caused by the high water partial pressure the concentration of the oxygen in the fuel cell will be additionally decreased and the performance will be reduced.. Therefore DLR has built-up an additional test facility for cell characterization for low pressures. The test facility can operate fuel cells down to an operating pressure of 20000 Pa (0.2 bar). In the test facility short stacks and single cells can be tested and investigated with the DLR tool for current density measurements as well as for electrochemical impedance spectroscopy can be integrated. The test facility is fully controlled by a programmable logic controller (PLC) which is also used for the data acquisition

Genetic analysis for a shared biological basis between migraine and coronary artery disease

OBJECTIVE: To apply genetic analysis of genome-wide association data to study the extent and nature of a shared biological basis between migraine and coronary artery disease (CAD). METHODS: Four separate methods for cross-phenotype genetic analysis were applied on data from 2 large-scale genome-wide association studies of migraine (19,981 cases, 56,667 controls) and CAD (21,076 cases, 63,014 controls). The first 2 methods quantified the extent of overlapping risk variants and assessed the load of CAD risk loci in migraineurs. Genomic regions of shared risk were then identified by analysis of covariance patterns between the 2 phenotypes and by querying known genome-wide significant loci. RESULTS: We found a significant overlap of genetic risk loci for migraine and CAD. When stratified by migraine subtype, this was limited to migraine without aura, and the overlap was protective in that patients with migraine had a lower load of CAD risk alleles than controls. Genes indicated by 16 shared risk loci point to mechanisms with potential roles in migraine pathogenesis and CAD, including endothelial dysfunction (PHACTR1) and insulin homeostasis (GIP). CONCLUSIONS: The results suggest that shared biological processes contribute to risk of migraine and CAD, but surprisingly this commonality is restricted to migraine without aura and the impact is in opposite directions. Understanding the mechanisms underlying these processes and their opposite relationship to migraine and CAD may improve our understanding of both disorders

Genetic analysis for a shared biological basis between migraine and coronary artery disease

OBJECTIVE: To apply genetic analysis of genome-wide association data to study the extent and nature of a shared biological basis between migraine and coronary artery disease (CAD). METHODS: Four separate methods for cross-phenotype genetic analysis were applied on data from 2 large-scale genome-wide association studies of migraine (19,981 cases, 56,667 controls) and CAD (21,076 cases, 63,014 controls). The first 2 methods quantified the extent of overlapping risk variants and assessed the load of CAD risk loci in migraineurs. Genomic regions of shared risk were then identified by analysis of covariance patterns between the 2 phenotypes and by querying known genome-wide significant loci. RESULTS: We found a significant overlap of genetic risk loci for migraine and CAD. When stratified by migraine subtype, this was limited to migraine without aura, and the overlap was protective in that patients with migraine had a lower load of CAD risk alleles than controls. Genes indicated by 16 shared risk loci point to mechanisms with potential roles in migraine pathogenesis and CAD, including endothelial dysfunction (PHACTR1) and insulin homeostasis (GIP). CONCLUSIONS: The results suggest that shared biological processes contribute to risk of migraine and CAD, but surprisingly this commonality is restricted to migraine without aura and the impact is in opposite directions. Understanding the mechanisms underlying these processes and their opposite relationship to migraine and CAD may improve our understanding of both disorders