Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

Background Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. Results We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being …

Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients

In this study, the circulating miRNome from diagnostic neuroblastoma serum was assessed for identification of noninvasive biomarkers with potential in monitoring metastatic disease. After determining the circulating neuroblastoma miRNome, 743 miRNAs were screened in 2 independent cohorts of 131 and 54 patients. Evaluation of serum miRNA variance in a model testing for tumor stage, MYCN status, age at diagnosis, and overall survival revealed tumor stage as the most significant factor impacting miRNA abundance in neuroblastoma serum. Differential abundance analysis between patients with metastatic and localized disease revealed 9 miRNAs strongly associated with metastatic stage 4 disease in b…

Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients

AbstractIn this study, the circulating miRNome from diagnostic neuroblastoma serum was assessed for identification of non-invasive biomarkers with potential in monitoring metastatic disease. After determining the circulating neuroblastoma miRNome, 743 miRNAs were screened in two independent cohorts of 131 and 54 patients. Evaluation of serum miRNA variance in a model testing for tumor stage, MYCN status, age at diagnosis and overall survival, revealed tumor stage as the most significant factor impacting miRNA abundance in neuroblastoma serum. Differential expression analysis between patients with metastatic and localized disease revealed 9 miRNAs strongly associated with metastatic stage 4 …

Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients.

Abstract Background Neuroblastoma is characterized by substantial clinical heterogeneity. Despite intensive treatment, the survival rates of high-risk neuroblastoma patients are still disappointingly low. Somatic chromosomal copy number aberrations have been shown to be associated with patient outcome, particularly in low- and intermediate-risk neuroblastoma patients. To improve outcome prediction in high-risk neuroblastoma, we aimed to design a prognostic classification method based on copy number aberrations. Methods In an international collaboration, normalized high-resolution DNA copy number data (arrayCGH and SNP arrays) from 556 high-risk neuroblastomas obtained at diagnosis were coll…

Diagnostics of autoimmune bullous diseases in German dermatology departments

Summary Background: No consistent data are available on the currently employed diagnostic tools for autoimmune bullous diseases in Germany. The aim of this survey was to describe currently performed diagnostic methods for bullous autoimmune diseases in German dermatology departments. Methods: A standardized questionnaire evaluated the available diagnostic methods i. e. direct immunofluorescence microscopy (IFM), indirect IFM, commercial ELISA systems, and non-commercial serological tests as well as the number of samples per year in all 34 university and 39 non-university dermatology departments. Results: The overall return rate was 89 %, 100 % and 79 % for the university and non-university …

Asynchronous Occlusion Culling on Heterogeneous PC Clusters for Distributed 3D Scenes

We present a parallel rendering system for heterogeneous PC clusters to visualize massive models. One single, powerful visualization node is supported by a group of backend nodes with weak graphics performance. While the visualization node renders the visible objects, the backend nodes asynchronously perform visibility tests and supply the front end with visible scene objects. The visualization node stores only currently visible objects in its memory, while the scene is distributed among the backend nodes’ memory without redundancy. To efficiently compute the occlusion tests in spite of that each backend node stores only a fraction of the original geometry, we complete the scene by adding h…

Segmental chromosomal alterations have prognostic impact in neuroblastoma: a report from the INRG project

Background: In the INRG dataset, the hypothesis that any segmental chromosomal alteration might be of prognostic impact in neuroblastoma without MYCN amplification (MNA) was tested. Methods: The presence of any segmental chromosomal alteration (chromosome 1p deletion, 11q deletion and/or chromosome 17q gain) defined a segmental genomic profile. Only tumours with a confirmed unaltered status for all three chromosome arms were considered as having no segmental chromosomal alterations. Results: Among the 8800 patients in the INRG database, a genomic type could be attributed for 505 patients without MNA: 397 cases had a segmental genomic type, whereas 108 cases had an absence of any segmental a…

Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study

Summary Background More accurate prognostic assessment of patients with neuroblastoma is required to better inform the choice of risk-related therapy. The aim of this study is to develop and validate a gene-expression signature to improve outcome prediction. Methods 59 genes were selected using an innovative data-mining strategy, and were profiled in the largest neuroblastoma patient series (n=579) to date using real-time quantitative PCR starting from only 20 ng of RNA. A multigene-expression signature was built using 30 training samples, tested on 313 test samples, and subsequently validated in a blind study on an independent set of 236 tumours. Findings The signature has a performance, s…

Revised risk estimation and treatment stratification of low- and intermediate-risk neuroblastoma patients by integrating clinical and molecular prognostic markers.

Abstract Purpose: To optimize neuroblastoma treatment stratification, we aimed at developing a novel risk estimation system by integrating gene expression–based classification and established prognostic markers. Experimental Design: Gene expression profiles were generated from 709 neuroblastoma specimens using customized 4 × 44 K microarrays. Classification models were built using 75 tumors with contrasting courses of disease. Validation was performed in an independent test set (n = 634) by Kaplan–Meier estimates and Cox regression analyses. Results: The best-performing classifier predicted patient outcome with an accuracy of 0.95 (sensitivity, 0.93; specificity, 0.97) in the validation coh…

Cyclodextrins in polymer synthesis: free radical polymerization of cyclodextrin complexes with oxazoline-functionalized vinyl monomers as guest molecules in aqueous medium

The synthesis of five new oxazoline functionalized vinyl monomers N-[4-(4′,5′-dihydrooxazol-2-yl)phenyl]acrylamide (3 a), N-[4-(4′,5′-dihydrooxazol-2-yl)phenyl]-2-methylacrylamide (3 b), N-{10-[4-(4′,5′-dihydrooxazol-2-yl)phenylcarbamoyl]decyl}-2-acrylamide (5 a), N-{10-[4-(4′,5′-dihydrooxazol-2-yl)phenylcarbamoyl]decyl}-2-methylacrylamide (5 b) and N-[4-(4′,5′-dihydrooxazol-2-yl)-phenyl]-4-vinylbenzamide (7) is described. With an equimolar amount of 2,6-dimethyl-β-cyclodextrin (DMCD) these monomers formed hydrophilic inclusion complexes 3 a,b-DMCD, 5 a,b-DMCD and 7-DMCD. These complexes were polymerized radically in an aqueous medium. Resulting polymers P-(3 a, b), P-(5 a, b) and P-(7) pre…

Diagnostik blasenbildender Autoimmundermatosen an deutschen Hautkliniken

Recommended practice for out-of-hospital emergency anaesthesia in adults: Statement from the Out-of-Hospital Emergency Anaesthesia Working Group of the Emergency Medicine Research Group of the German Society of Anaesthesiology and Intensive Care.

Emergency anaesthesia is an important therapeutic measure in out-of-hospital emergency medicine. The associated risks are considerably higher than those of in-hospital anaesthesia. The primary objectives of emergency anaesthesia are hypnosis, analgesia, oxygenation and ventilation through airway management. The secondary objectives of emergency anaesthesia are amnesia, anxiolysis, the reduction of oxygen consumption and respiratory work, the protection of vital organs and the avoidance of secondary myocardial and cerebral damage. A critical evaluation of the indications for outof- hospital emergency anaesthesia must take into consideration patient, case and provider-related factors. Rapid s…