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:Whole-genome sequencing on PacBio of laboratory mouse strains. See http://www.sanger.ac.uk/resources/mouse/genomes/ for more details. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Project description:A previously described low-fitness, high stress-resistant, variant of Listeria monocytogenes LO28 WT was subjected to an experimental evolution regime, selecting (in two parallel lines) for increased fitness in unstressed conditions. Evolved variants with increased fitness reverted to WT-like stress resistance. Whole genome sequencing and proteomics were used to identify differences between the ancestral and evolved strains.
Project description:Low coverage whole-genome sequencing have been performed on uterine leiomyosarcoma to uncovered novel potential driver genes and recurrently affected pathways.
Project description:We sequenced two tumor/normal pairs obtained from two paediatric medulloblastoma patients (MB14 and MB24) with at least 30x coverage on all commonly used next-generation sequencing platforms for whole genome sequencing (SOLiD 4, 5500xl SOLiD, Illumina's HiSeq2000, and Complete Genomic' technology). The normal tissue samples came from venous blood. We compared their ability to call single nucleotide variations (SNVs) in whole-genome sequencing data with high confidence. As gold standard for SNV calling, we used genotypes determined by Affymetrix SNP 6.0 Array Technology (total of 907,551 SNPs after quality filtering).
Project description:Whole genome sequencing of 10 HCLc tumor and matched-germline T cells. Genomic DNA from highly purified HCLc tumor and T cell populations were utilized for library preparation using NEBNext Ultra DNA library prep kit. Sequencing was performed as 150 bp paired end sequencing using four lanes of an Illumina HiSeq4000 to an average depth of 12X. Reads from each library were aligned to the human reference genome GRCh37 using BWA-MEM (v0.7.12). The analysis of somatic genetic alterations in WGS data from tumor-germline pair HCLc samples was divided based on the nature of the mutation, as follow: single-nucleotide variants (SNVs), indels, CNAs and SVs. Moreover, COSMIC mutational signatures and subclonal architecture was inferred for each tumor.
Project description:To understand the behaviour in terms of special genome components that are expressed by L.monocytogenes in the presence of another bacterium as may be the condition in its natural environments was our objective, for which we have used microarray gene expression at different time intervals of growth from 4hrs to 24 hrs. Expression of L.monocytogenes as co-cultures, both in broth culture state and biofilm state were differentiated to that of 24hrs pure broth culture. Also genes regulated for and during biofilm formation as pure cultures were identified with comparision to 24hrs pure broth culture. Distinguishing features with notable variation in all of the three sample sets as L.monocytogenes in pure culture biofilm, co-culture broth and co-culture biofilm were observable. Genes that are specifically up-regulated at each of growth condition and time interval were identified, genes regulated with ascending and descending patterns in time were also noticable. These variation in the gene expression gives an insight into the alterations in the biosynthetic and metabolic pathways under different states of growth Agilent one-color experiment,Organism: Listeria monocytogenes , Genotypic Technology Pvt. Ltd. designed Custom Microarray Listeria monocytogenes 8x15k (Agilent-30831) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
