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:The intent of the experiment was to infer, from re-sequencing of genomic DNA, the coordinates of neo-insertions from activated ONSEN/COPIA78 LTR retrotrasnposon in Arabidopsis thaliana. For this, we performed Illumina 75 bp pair-end PCR-free DNA genome re-sequencing in several independent lines of RdDM mutant nrpd1-3.
Project description:The intent of the experiment was to infer from DNA sequencing the occurrence of extra-chromosomal DNA from Arabidopsis thaliana's heat-activated LTR retrotransposon Onsen/COPIA78. For this, we performed Illumina 150 bp pair-end PCR-free DNA genome re-sequencing, in both wild-type Col-0 and RdDM mutant nrpd1-3 under control and heat stress.
Project description:This study aimed to evaluate the cost-effective and genome-wide cell-free reduced representation bisulfite sequencing (cfRRBS) method combined with computational deconvolution for effective disease monitoring in patients with esophageal adenocarcinoma (EAC). cfDNA methylation profiling with cfRRBS was performed on 162 blood plasma samples from 33 EAC cancer patients and 28 blood plasma samples from 20 healthy donors. In addition, for reproducibility testing purposes of the method, 9 plasma samples were re-prepped (library was re-made) and re-sequenced once (n=9) or twice (n=1). As a reference for the data deconvolution cfRRBS was performed on 7 EAC tumor tissue (FFPE) samples.
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:In this study, we used high-resolution mass spectrometry followed by proteogenomic mapping to achieve genome re-annotation of CyHV-2.
Project description:DNA replication must be tightly controlled during each cell cycle to prevent unscheduled replication and ensure proper genome maintenance. The currently known controls that prevent re-replication act redundantly to inhibit pre-Replicative Complex (pre-RC) assembly outside of the G1 phase of the cell cycle. We have analyzed the effects of re-replication on the S. cerevisiae genome using a combination of Comparitive Genomic Hybridization (CGH) of re-replicating strains and Genome-Wide Location Analysis of pre-RC components. These data indicate which sites in the genome assemble pre-RCs under re-replication conditions, which sites undergo re-initiation and the extent of re-replication. Keywords: comparative genomic hybridization, ChIP-chip, re-replication, DNA replication, pre-RC
Project description:The study is intended to collect specimens to support the application of genome analysis technologies, including large-scale genome sequencing. This study will ultimately provide cancer researchers with specimens that they can use to develop comprehensive catalogs of genomic information on at least 50 types of human cancer. The study will create a resource available to the worldwide research community that could be used to identify and accelerate the development of new diagnostic and prognostic markers, new targets for pharmaceutical interventions, and new cancer prevention and treatment strategies. This study will be a competitive enrollment study conducted at multiple institutions.