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:To evaluate the impacts of Dnmt3A mutation in the methylome of male germ cells, mutant and control whole genome bisulfite sequencing experiments were conducted starting from genomic DNA obtained from FACS-sorted germ cells.
Project description:Null mutations for genes encoding the major seed storage protein in pea, vicilin, were sought among a fast-neutron mutant population. Combinations of four and five mutations, where individual vicilin loci had been deleted, were generated to address the question of how removal or reduction of a major storage protein would impact on seed protein concentration and yield. While seed protein concentrations were not reduced in mutant lines, indicative of a re-balancing of the proteome, there were notable differences in their metabolite, proteomic and amino acid profiles. The genomic regions which were deleted were defined by whole genome sequencing of the parental line, JI2822 and its quintuple vicilin null derivative.
Project description:Null mutations for genes encoding the major seed storage protein in pea, vicilin, were sought among a fast-neutron mutant population. Combinations of four and five mutations, where individual vicilin loci had been deleted, were generated to address the question of how removal or reduction of a major storage protein would impact on seed protein concentration and yield. While seed protein concentrations were not reduced in mutant lines, indicative of a re-balancing of the proteome, there were notable differences in their metabolite, proteomic and amino acid profiles. The genomic regions which were deleted were defined by whole genome sequencing of the parental line, JI2822 and its quintuple vicilin null derivative.
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:An induced-mutant line derived from the elite rice cultivar, Samba Mahsuri, was identified to exhibit broad-spectrum resistance to BB. Using next-generation gene mapping approaches, we identified a genomic interval in chromosome 6 to be linked to BB resistance. Analysis of the SNPs in the locus and subsequent linkage analysis indicated that a missense SNP located in the second exon of the Mitogen-Activated Protein Kinase 6 (OsMAPK6) could be the causal mutation. A detailed examination of OsMAPK6 gene sequences in over 4000 rice genomes revealed that the mutant allele identified in this study is novel to rice germplasm. The candidate SNP causes the substitution of an invariant Serine residue with a Proline residue (S84P), thus likely affecting the protein function. Global transcriptome, metabolome, biochemical, and molecular analyses suggested that BB42 exhibit autoimmunity.
Project description:Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in rdm16ros1, ros1, nrpd1ros1 mutants and examine the effect of RDM16 on DNA methylation 4 samples examined: C24 wild type with RD29A-LUC transgene, rdm16ros1 double mutant, ros1 mutant, nrpd1ros1 mutant (all in C24 background with RD29A-LUC transgene)