Project description:The P. gingivalis 33277 transposon mutant J5-c5, isolated in this study, was demonstrated to exhibit a lipid A deacylase phenotype. The mutant is unable to deacylate lipid A, which confers to it, in stark contrast to wild-type, an inability to evade the powerful TLR4 innate immune response. The mutant was shown to contain five transposons. In order to determine the affected gene responsible for this phenotype, we took the approach of comparing gene expression between wild-type and J5-c5 transposon mutant. RNA was extracted from three separate biological samples of each strain and RNAseq performed using Illumina’s HiSeq sequencing facility at the University of Washington Center for Precision Diagnostics. RNAseq data was analyzed closely following guidance outlined in Law et al (doi:10.12688/f1000research.9005.2).
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).
