Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:In this research, Pseudomonas aeruginosa underwent evolution in the supernatant of either S. aureus (SA) or K. pneumoniae (KP). Through this evolution process, we enriched a sufficient number of bacterial cells along with their corresponding proteins. Following 15 cultivation cycles, notable changes were observed in the phenotypes of P. aeruginosa, with a series of mutations identified through whole-genome sequencing (WGS). Proteomics analysis unveiled that the supernatant-evolved mutants displayed distinct regulation patterns in crucial pathways (including the type VI secretion system, biofilm formation, phenazine biosynthesis, translation, beta-lactam resistance, and O-antigen biosynthesis) in comparison to both the ancestral strain and the unmodified medium-evolved (UmMd-evolved) strain.
Project description:The proteome of the SS13 isolate assigned to the Chromatiaceae family was assessed by shotgun proteomics using a pan-proteomics database for the genus Rheinheimera and a whole genome sequencing -derived database.
Project description:BackgroundCross-border healthcare may promote the spread of multidrug-resistant microorganisms (MDRO) and is challenging due to heterogeneous antimicrobial resistance (AMR) prevention measures (APM). The aim of this article is to compare healthcare workers (HCW) from Germany (DE) and The Netherlands (NL) on how they perceive and experience AMR and APM, which is important for safe patient exchange and effective cross-border APM cooperation.MethodsA survey was conducted amongst HCW (n = 574) in hospitals in DE (n = 305) and NL (n = 269), using an online self-administered survey between June 2017 and July 2018. Mann-Whitney U tests were used to analyse differences between answers of German and Dutch physicians (n = 177) and German and Dutch nurses (n = 397) on 5-point Likert Items and Scales.ResultsSimilarities between DE and NL were a high awareness about the AMR problem and the perception that the possibility to cope with AMR is limited (30% respondents perceive their contribution to limit AMR as insufficient). Especially Dutch nurses scored significantly lower than German nurses on their contribution to limit AMR (means 2.6 vs. 3.1, p ≤ 0.001). German HCW were more optimistic about their potential role in coping with AMR (p ≤ 0.001), and scored higher on feeling sufficiently equipped to perform APM (p ≤ 0.003), although the mean scores did not differ much between German and Dutch respondents.ConclusionsAlthough both German and Dutch HCW are aware of the AMR problem, they should be more empowered to contribute to limiting AMR through APM (i.e. screening diagnostics, infection diagnosis, treatment and infection control) in their daily working routines. The observed differences reflect differences in local, national and cross-border structures, and differences in needs of HCW, that need to be considered for safe patient exchange and effective cross-border APM.