Ontology highlight
ABSTRACT:
PROVIDER: PRJNA947257 | ENA |
REPOSITORIES: ENA
Similar Datasets
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).
| 2533916 | ecrin-mdr-crc
Project description:The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the NCI-60 have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy. To approach a functional understanding of these sequences in transformed cells, we used transposon insertion profiling (TIP) to map Long INterspersed Element-1 (LINE-1, L1) and Alu Short INterspersed Element (SINE) insertions in cancer genes in NCI-60 cells. As expected, this identified known insertions, polymorphisms shared in unrelated tumor cell lines, as well as unique, potentially tumor-specific insertions. Here, we report a map of these insertion sites and conduct association analyses relating individual insertions to a variety of cellular phenotypes.
2017-02-09 | GSE83756 | GEO
Project description:The Complex Architecture of Transgene Insertions
| PRJNA427134 | ENA
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)
2013-09-27 | E-GEOD-44417 | biostudies-arrayexpress
Project description:The high level of human genome structural variation among individuals suggests that there must be portions of the genome that have yet to be discovered, annotated and characterized at the sequence level. Using clone resources developed as part of the Human Genome Structural Variation Sequencing Project, we focused on the characterization of 2,363 novel sequence contigs not present in the human reference genome. We determined that these contigs corresponded to 720 distinct loci of which 400 now have an anchored position in the reference genome. We investigated the sequence properties of these loci and determined that 37% of these novel insertions are copy-number polymorphic. We find that they are significantly enriched within the last 5 Mb of chromosomes (a 2.9-fold enrichment, p=1.0e-18, binomial test) and that most arose as a result of deletions in the human lineage after separation from the African great apes. A subset of these sites shows evidence of marked population stratification among Asian, African and European populations, including a 3.9-kb insertion within the first intron of the lactase gene. Complete sequencing of clones from 192 genomic loci, including 156 completely spanned insertions, provides a detailed and contextual view of 1.67 Mb of inserted sequence. Analysis of this sequence identified 477 elements that show evidence of sequence constraint over evolutionary time, as well as matches to 22 RefSeq gene segments. Twenty-six of the insertions contain matches against mRNA-seq data indicating the potential presence of functionally important, unannotated human sequences. Taking advantage of this high-quality sequence, we develop a method to accurately genotype these novel insertions using next-generation whole-genome sequencing datasets.
2010-04-20 | GSE20634 | GEO
Project description:A reporter transgene displayed parental imprinting in mouse embryos when positioned into the Itga6 gene. The strong lacZ pattern of expression scored in embryos inheriting the transgene from a male was not present when transmitted from a female. The transgene exhibited maternal allele-specific DNA hyper-methylation acquired in the germ-line and histone modifications corresponded to profiles described at known imprinted loci. Chromosome conformation analyzes revealed distinct, parent-of-origin interaction domains, with a more compact structure characterizing the maternally inherited repressed allele. The analysis of such transgene insertions with a selective potential to induce imprinting may help understanding the mechanisms identifying particular loci as targets for allele-specific repression.
2013-07-03 | GSE48148 | GEO
Project description:Whole-genome DNA libraries were prepared from a population of just under 100 Col/Ler F1 backcrossed to Col. Low-coverage whole-genome sequencing was used to map meiotic crossovers in this population following the protocol described in Rowan et al., 2015, doi: 10.1534/g3.114.016501.
2015-10-15 | E-MTAB-3926 | biostudies-arrayexpress
Project description:Somatic transposon mutagenesis in mice is an efficient strategy to investigate the genetic mechanisms of tumorigenesis. The identification of tumor driving transposon insertions traditionally requires the generation of large tumor cohorts to obtain information about common insertion sites. Tumor driving insertions are also characterized by their clonal expansion in tumor tissue, a phenomenon that is facilitated by the slow and evolving transformation process of transposon mutagenesis. We describe here an improved approach for the detection of tumor driving insertions that assesses the clonal expansion of insertions by quantifying the relative proportion of sequence reads obtained in individual tumors. To this end, we have developed a protocol for insertion site sequencing that utilizes acoustic shearing of tumor DNA and Illumina sequencing. We analyzed various solid tumors generated by PiggyBac mutagenesis and for each tumor >10^6 reads corresponding to >10^4 insertion sites were obtained. In each tumor, 9 to 25 insertions stood out by their enriched sequence read frequencies when compared to frequencies obtained from tail DNA controls. These enriched insertions are potential clonally expanded tumor driving insertions, and thus identify candidate cancer genes. The candidate cancer genes of our study comprised many established cancer genes, but also novel candidate genes such as Mastermind-like1 (Mamld1) and Diacylglycerolkinase delta (Dgkd). We show that clonal expansion analysis by high-throughput sequencing is a robust approach for the identification of candidate cancer genes in insertional mutagenesis screens on the level of individual tumors. Solid tumors in mice were generated by somatic transposon mutagenesis with a PiggyBac transposon system. Insertion sites of transposons in 11 tumors and 6 non-cancerous tail controls were determined by Illumina high-throughput sequencing. Insertions were determined both on 5' and 3' sides of the transposon (PB5 and PB3, respectively). Quantitative analysis of read numbers revealed enrichment of certain insertions in tumors, but not in controls, and these enriched insertions identify candidate cancer genes.
2013-08-28 | E-GEOD-46210 | biostudies-arrayexpress
Project description:Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. Likewise, advances in mass spectrometry proteomics now permit highly sensitive and accurate studies of protein expression at the proteome-scale. However, most proteomic studies remain limited to the analysis of canonical reference proteomes. Here, we develop ProteomeGenerator2 (PG2), based on the scalable and modular ProteomeGenerator framework. PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2.
2024-05-22 | PXD037061 | Pride