Ena-DATASET-UH-tumorgenomics-12-09-2018-10:44:16:496-468 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001004329 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The dataset contains somatic variants in 344 colorectal cancer samples. Variants are called with Mutect2 (GRCh38).
Important: VCF-files include also variants, which have been annotated as "str_contraction" and "panel_of_normals".
Please, use only "PASS" variants in studies, which are not microsatellite repeat related. Samples are sequenced
with Novaseq 6000, HiSeq 2000, and HiSeq X Ten instruments (average coverage depth ~30+). The dataset consists of
257 MSS, 58 MSI, 25 MSS IBD, and 4 POLE mutant CRCs.
| EGAD00001006572 | EGA
Project description:Among the examined genes, none of genes associated with high frequency microsatellite instability (MSI-H) in the panel was mutated (MLH1, MSH2, POLE). In addition, clustering analyses based on RNA-seq data indicated that expression profiles of the spheroids were more similar to colon cancer cells in the CMS-2 and CMS-3 category than those in the MSI-H-related CMS-1. These data suggested that all the examined spheroids were associated with microsatellite stable (MSS) phenotype.
2021-02-25 | GSE167395 | GEO
Project description:The POLE mutations represent high somatic mutation loads in patients with colorectal cancer, especially in those with MMR proficient or MSS, therefore, tumors harbouring POLE mutations might be susceptible to immune checkpoint blockade.
Based on these reasons, the investigators planned a phase II study of durvalumab monotherapy in patients with previously treated, metastatic, MMR deficient (MSI-H) or POLE mutated colorectal cancer.
| 2266020 | ecrin-mdr-crc
Project description:The POLE mutations represent high somatic mutation loads in patients with colorectal cancer, especially in those with MMR proficient or MSS, therefore, tumors harbouring POLE mutations might be susceptible to immune checkpoint blockade.
Based on these reasons, Investigator planned a phase II study of avelumab monotherapy in patients with previously treated, metastatic, MMR deficient (MSI-H) or POLE mutated colorectal cancer.
| 2244190 | ecrin-mdr-crc
Project description:modENCODE_submission_2565 This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: The White Lab is aiming to map the association of many of the non-histone chromosomal proteins on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation-on-chip (ChIP-on-chip) utilizing whole-genome tiling arrays. The data generated by ChIP-chip experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested chromatin-binding protein. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf CHIP-chip
2010-12-10 | GSE25962 | GEO
Project description:DNA polymerase epsilon (Pol epsilon) plays multiple roles in genome duplication and its catalytic subunit POLE suppresses tumorigenesis in humans. Despite its importance, we have limited understanding of Pol epsilon functional mechanisms and how its loss-of-function affects the evolution of cancer genomes. To address this issue, we used the budding yeast ortholog Pol2 to model cancer-associated POLE mutations that affect an uncharacterized yet highly conserved Pol2/POLE family-specific region. Analysis of pol2 mutants revealed an unexpected role for this region in the incorporation of Pol epsilon into the pre-loading complex during replisome assembly. Cellular and reconstitution experiments further identified a separate role for this region in promoting Pol epsilon polymerase activity. Unlike previously reported POLE mutations leading to hypermutation in cancer cells, the examined pol2 variants increase gross chromosomal rearrangements but not mutation rates. Our findings thus suggest that the Pol epsilon catalytic core integrates replisome assembly and DNA polymerization functions and that POLE tumor suppressive roles likely extend beyond limiting replication errors.
2020-03-29 | GSE132450 | GEO
Project description:Mutations in non-essential RSC genes was shown to cause spontaneous diploidization due to defective spindle pole body (SPB) duplication. RNA sequencing was performed to assess whether these effects were due to altered transcript profiles in rsc mutants
2018-05-30 | GSE106768 | GEO
Project description:Cohesin, a chromatin-associated protein complex with four core subunits (Smc1a, Smc3, Rad21 and either Stag1 or 2), has a central role in cell proliferation and gene expression in metazoans. Human developmental disorders termed “cohesinopathies” are characterised by germline mutations in cohesin or its regulators that do not entirely eliminate cohesin function. However, it is not clear if mutations in individual cohesin subunits have independent developmental consequences. Using zebrafish rad21 or stag2 mutants to change cohesin complex quantity or composition, we show that these parameters independently influence embryonic tailbud development. Both mutants have altered mesoderm induction, but only homozygous or heterozygous rad21 mutation affects cell cycle gene expression. stag2 mutants have slimmer notochords and reduced Wnt signaling in neuromesodermal progenitors as revealed by single cell RNA-sequencing. Stimulation of Wnt signaling rescues transcription and morphology in stag2, but not rad21 mutants, implying that individual cohesin mutations respond independently to cell signaling. Our results have implications for the understanding and management of cohesinopathies.
2023-11-29 | GSE247246 | GEO