MTPpilot: An Interactive Software for Visualization of Next-Generation Sequencing Results in Molecular Tumor Boards

PURPOSE Comprehensive targeted next-generation sequencing (NGS) panels are routinely used in modern molecular cancer diagnostics. In molecular tumor boards, the detected genomic alterations are often discussed to decide the next treatment options for patients with cancer. With the increasing size and complexity of NGS panels, the discussion of these results becomes increasingly complex, especially if they are reported in a text-based form, as it is the standard in current molecular pathology. METHODS We have developed the Molecular Tumor Profiling pilot (MTPpilot) webservice using HTML, PHP, JavaScript, and MySQL to support the clinical discussion of NGS results at molecular tumor boards. RESULTS MTPpilot integrates various public genome, network, and cancer mutation databases with interactive visualization tools to assess the functional impact of mutations and support clinical decision making at tumor boards. CONCLUSION MTPpilot is tailored for discussion of NGS gene panel results at molecular tumor boards. It is freely available as a webservice at MTPpilot

Longitudinal study of the effects of teat condition on the risk of new intramammary infections in dairy cows

Machine milking–induced alterations of teat tissue may impair local defense mechanisms and increase the risk of new intramammary infections. The objective of the current study was to assess the influence of short-term and long-term alterations of teat tissue and infectious status of the udder quarter on the risk of naturally occurring new intramammary infections, inflammatory responses, and mastitis. Short-term and long-term changes in teat condition of right udder quarters of 135 cows of a commercial dairy farm in Saxony-Anhalt, Germany, were recorded monthly for 10 mo using simple classification schemes. Quarter milk samples were collected from all examined quarters at each farm visit. Bacteriological culture results and somatic cell counts of quarter milk samples were used to determine new inflammatory responses (increase from ≤100,000 cells/mL to >100,000 cells/mL between 2 samples), new infections (detection of a pathogen from a quarter that was free of the same pathogen at the preceding sampling), and new mastitis (combination of new inflammatory response and new infection). Separate Poisson mixed models for new inflammatory responses, new infections, and new mastitis caused by specific pathogens or groups of pathogens (contagious, environmental, major, minor, or any) were used to estimate risk ratios and 95% confidence intervals. Data preparation and parameter estimation were performed using the open source statistical analysis software R. We observed no effect of any variable describing teat condition on the risk of new intramammary infections, inflammatory responses, or mastitis. Intramammary infections of the same udder quarter in the preceding month did not affect risk either

Improving the turnaround time of molecular profiling for advanced non-small cell lung cancer: Outcome of a new algorithm integrating multiple approaches

BACKGROUND Molecular tumor profiling to identify oncogenic drivers and actionable mutations has a profound impact on how lung cancer is treated. Especially in the subgroup of non-small cell lung cancer (NSCLC), molecular testing for certain mutations is crucial in daily clinical practice and is recommended by international guidelines. To date, a standardized approach to identify druggable genetic alterations are lacking. We have developed and implemented a new diagnostic algorithm to harmonize the molecular testing of NSCLC. PATIENTS AND METHODS In this retrospective analysis, we reviewed 119 patients diagnosed with NSCLC at the University Hospital Zurich. Tumor samples were analyzed using our standardized diagnostic algorithm: After the histological diagnosis was made, tissue samples were further analyzed by immunohistochemical stainings as well as the real-time PCR test Idylla™. Extracted DNA was further utilized for comprehensive genomic profiling (FoundationOne®CDx, F1CDx). RESULTS Out of the 119 patients were included in this study, 100 patients were diagnosed with non-squamous NSCLC (nsqNSCLC) and 19 with squamous NSCLC (sqNSCLC). The samples from the nsqNSCLC patients underwent testing by Idylla™ and were evaluated by immunohistochemistry (IHC). F1CDx analysis was run on 67 samples and 46 potentially actionable genomic alterations were detected. Ten patients received the indicated targeted treatment. The median time to test results was 4 days for the Idylla test, 5 days for IHC and 13 days for the F1CDx. CONCLUSION In patients with NSCLC, the implementation of a standardized molecular testing algorithm provided information on predictive markers for NSCLC within a few working days. The implementation of broader genomic profiling led to the identification of actionable targets, which would otherwise not have been discovered

ROS1 genomic rearrangements are rare actionable drivers in microsatellite stable colorectal cancer

c-Ros oncogene 1, receptor tyrosine kinase (ROS1) genomic rearrangements have been reported previously in rare cases of colorectal cancer (CRC), yet little is known about the frequency, molecular characteristics, and therapeutic vulnerabilities of ROS1-driven CRC. We analyzed a clinical dataset of 40 589 patients with CRC for ROS1 genomic rearrangements and their associated genomic characteristics (Foundation Medicine, Inc [FMI]). We moreover report the disease course and treatment response of an index patient with ROS1-rearranged metastatic CRC. ROS1 genomic rearrangements were identified in 34 (0.08%) CRC samples. GOPC-ROS1 was the most common ROS1 fusion identified (11 samples), followed by TTC28-ROS1 (3 samples). Four novel 5' gene partners of ROS1 were identified (MCM9, SRPK1, EPHA6, P4HA1). Contrary to previous reports on fusion-positive CRC, ROS1-rearrangements were found exclusively in microsatellite stable (MSS) CRCs. KRAS mutations were significantly less abundant in ROS1-rearranged vs ROS1 wild type cases. The index patient presented with chemotherapy-refractory metastatic right-sided colon cancer harboring GOPC-ROS1. Molecularly targeted treatment with crizotinib induced a rapid and sustained partial response. After 15 months on crizotinib disseminated tumor progression occurred and KRAS Q61H emerged in tissue and liquid biopsies. ROS1 rearrangements define a small, yet therapeutically actionable molecular subgroup of MSS CRC. In summary, the high prevalence of GOPC-ROS1 and noncanonical ROS1 fusions pose diagnostic challenges. We advocate NGS-based comprehensive molecular profiling of MSS CRCs that are wild type for RAS and BRAF and patient enrollment in precision trials. Keywords: ROS1 rearrangement; acquired resistance; colorectal cancer; crizotinib; molecular subgroups; precision treatmen

ROS1 genomic rearrangements are rare actionable drivers in microsatellite stable colorectal cancer.

c-Ros oncogene 1, receptor tyrosine kinase (ROS1) genomic rearrangements have been reported previously in rare cases of colorectal cancer (CRC), yet little is known about the frequency, molecular characteristics, and therapeutic vulnerabilities of ROS1-driven CRC. We analyzed a clinical dataset of 40 589 patients with CRC for ROS1 genomic rearrangements and their associated genomic characteristics (Foundation Medicine, Inc [FMI]). We moreover report the disease course and treatment response of an index patient with ROS1-rearranged metastatic CRC. ROS1 genomic rearrangements were identified in 34 (0.08%) CRC samples. GOPC-ROS1 was the most common ROS1 fusion identified (11 samples), followed by TTC28-ROS1 (3 samples). Four novel 5' gene partners of ROS1 were identified (MCM9, SRPK1, EPHA6, P4HA1). Contrary to previous reports on fusion-positive CRC, ROS1-rearrangements were found exclusively in microsatellite stable (MSS) CRCs. KRAS mutations were significantly less abundant in ROS1-rearranged vs ROS1 wild type cases. The index patient presented with chemotherapy-refractory metastatic right-sided colon cancer harboring GOPC-ROS1. Molecularly targeted treatment with crizotinib induced a rapid and sustained partial response. After 15 months on crizotinib disseminated tumor progression occurred and KRAS Q61H emerged in tissue and liquid biopsies. ROS1 rearrangements define a small, yet therapeutically actionable molecular subgroup of MSS CRC. In summary, the high prevalence of GOPC-ROS1 and noncanonical ROS1 fusions pose diagnostic challenges. We advocate NGS-based comprehensive molecular profiling of MSS CRCs that are wild type for RAS and BRAF and patient enrollment in precision trials

Charakterisierung der molekularen Wechselwirkung zwischen Calmodulin und Zieldomänen : eine Oberflächen-Plasmon-Resonanz spektroskopische Studie

Calmodulin (CaM) ist ein ubiquitärer Calciumsensor in Zellen. Bei einem Anstieg der intrazellulären Ca$^{2+}$-Konzentration binden Ca$^{2+}$-Ionen am CaM und induzieren eine Konformationsänderung des Proteins. Das Ca$^{2+}$/CaM interagiert mit einer Vielzahl von Zielproteinen, die bei einer Bindung aktiviert werden. Die CaM-bindende Domäne in den Zielproteinen umfaßt meist ein 14 Aminosäuren (AS) langes Peptidsegment, dessen AS-Sequenz aber von Protein zu Protein sehr unterschiedlich sein kann. Einige gemeinsame Merkmale besitzen aber alle CaM-Bindestellen: (1) hydrophobe AS in den Positionen 1 und 14, häufig auch in den Positionen 5 und 8, (2) überdurchschnittlich viele basische AS und (3) die Tendenz der Polypeptidkette, sich $\alpha$-helical zu falten. Die Dissoziationskonstantenkönnen um mehrere Zehnerpotenzen variieren (subnanomolarer Bereich bis zu einigen $\mu$M). In dieser Arbeit wurde untersucht, welche molekularen Determinanten wie z.B. die AS-Sequenz, benachbarte Domänen oder Phosphorylierungen die Bindung von CaM an Zielproteine bestimmen. Die Bestimmung der Dissoziationskonstanten erfolgte mit Hilfe der Oberflächen-Plasmon-Resonanz (SPR) Spektroskopie, einer Methode, um Protein-Protein Wechselwirkungen zeitaufgelöst zu analysieren. $\textbf{Wechselwirkung von NO-Synthasen mit CaM}$ Es sind drei verschiedene Isoformen der NO-Synthasen (NOS) bekannt, die alle CaMals Cofaktor für die Synthese von Stickoxid (NO) benötigen. Allerdings werden die drei Isoformen unterschiedlich reguliert. Die Aktivität der neuronalen NOS-I und der endothelialen NOS-III werden über die intrazelluläre Ca$^{2+}$-Konzentration reguliert, die NOS-II aus Macrophagen ist unabhängig von der Ca$^{2+}$-Konzentration in der Zelle aktiv. Peptide, die die CaM-Bindestellen der NOS-I und NOS-lI repräsentieren, wurden synthetisiert und in der Dextranmatrix eines Sensorchips immobilisiert. Der Bindung von CaM an das immobilisierte Peptid aus der NOS-I ergab eine Dissoziationskonstante von 5 nM. Die Bindung von CaM an ein Peptid aus der NOS-II zeigte ein völlig anderes Verhalten. Die Dissoziationskonstante lag im subnanomolaren Bereich (< 0,1 nM). Selbst in Abwesenheit von Ca$^{2+}$ konnte eine CaM-Bindung an das immobilisierte Peptid beobachtet werden. Punktmutationen an den CaM-Bindestellen der NOS-I und NOS-lI zeigten, daß ein Lysin in Position 13 für eine Ca$^{2+}$-abhängige Bindung von CaM wichtig ist. Die CaM-Bindestelle der NOS-I besitzt eine putative Phosphorylierungsstelle für Proteinkinasen. Ein phosphoryliertes Peptid, das diese CaM-Bindestelle repräsentiert, zeigte keine Bindung zu CaM mehr. $\textbf{Wechselwirkung von cyclisch Nukleotid-gesteuerten Ionenkanälen mit CaM}$ Die cyclisch Nukleotid-gesteuerten Ionenkanäle [...

ACON - Adaptive Control Schlussbericht

SIGLEAvailable from TIB Hannover: F01B187 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekBundesministerium fuer Bildung, Wissenschaft, Forschung und Technologie, Bonn (Germany)DEGerman

Ladungswechsel- und Verbrennungsoptimierung schnellaufender Zweitakt-Dieselmotoren zur Reduzierung der Laerm- und Abgasemissionen und des Betriebsstoffverbrauches Schlussbericht

Two stroke diesel engines are established as being the most efficient prime movers (e.g. they are the main propulsion technology used in large marine vessels). This technology is not yet available in smaller sizes. Therefore the main principles of fast running, turbocharged, two-stroke diesel engines have been investigated in the project 'Optimisation of Scavenging, Combustion and Emissions of fast running Two-Stroke Diesel Engines' in order to achieve significant improvements of the efficiency while reducing emissions. In many steps the engine components involved in these fields of interest have been optimised in their design as well as tested on elaborate bench tests. Thereby an improvement of consumption, scavenging, combustion and emissions could be achieved. Along the possible use in the field of general aviation, these results might be applicable to other fields; a reduction of emissions and consumption are not only interesting in their use for two stroke diesels. Individual results, e.g. the improved injection or turbocharging might very well benefit the further development of four strokes engines. (orig.)SIGLEAvailable from TIB Hannover: F00B790 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekBundesministerium fuer Bildung und Forschung (BMBF), Bonn (Germany)DEGerman