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Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE92271 | GEO | 2016/12/13

SECONDARY ACCESSION(S): PRJNA357064

REPOSITORIES: GEO

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Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig8b]

Project description:Copy number alteration in out-growing mouse tumor cells comparing that in the original tumor cells that was primarily inoculated into the indicated mice. Goal is to determine the effects of IFN-gamma producing tumor-specific CTL on targeted tumor cell gene expression.

2016-12-13 | GSE92270 | GEO

Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig7b]

2016-12-13 | GSE92269 | GEO

Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig5b]

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Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig5a]

2016-12-13 | GSE92267 | GEO

Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig3b]

2016-12-13 | GSE92266 | GEO

Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig3a-b]

2016-12-13 | GSE92265 | GEO

Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells [Fig3a-a]

2016-12-13 | GSE92264 | GEO

Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells

Project description:Copy number alteration in Murine Tumor Cells: primary inoculated tumor cells vs. out-growing tumor cells

| PRJNA357064 | ENA

Pan-cancer patterns of somatic copy number alteration.

Project description:Determining how somatic copy number alterations (SCNAs) promote cancer is an important goal. We characterized SCNA patterns in 4,934 cancers from The Cancer Genome Atlas Pan-Cancer data set. Whole-genome doubling, observed in 37% of cancers, was associated with higher rates of every other type of SCNA, TP53 mutations, CCNE1 amplifications and alterations of the PPP2R complex. SCNAs that were internal to chromosomes tended to be shorter than telomere-bounded SCNAs, suggesting different mechanisms underlying their generation. Significantly recurrent focal SCNAs were observed in 140 regions, including 102 without known oncogene or tumor suppressor gene targets and 50 with significantly mutated genes. Amplified regions without known oncogenes were enriched for genes involved in epigenetic regulation. When levels of genomic disruption were accounted for, 7% of region pairs were anticorrelated, and these regions tended to encompass genes whose proteins physically interact, suggesting related functions. These results provide insights into mechanisms of generation and functional consequences of cancer-related SCNAs.

| S-EPMC3966983 | biostudies-literature

Copy number alteration burden predicts prostate cancer relapse.

Project description:Primary prostate cancer is the most common malignancy in men but has highly variable outcomes, highlighting the need for biomarkers to determine which patients can be managed conservatively. Few large prostate oncogenome resources currently exist that combine the molecular and clinical outcome data necessary to discover prognostic biomarkers. Previously, we found an association between relapse and the pattern of DNA copy number alteration (CNA) in 168 primary tumors, raising the possibility of CNA as a prognostic biomarker. Here we examine this question by profiling an additional 104 primary prostate cancers and updating the initial 168 patient cohort with long-term clinical outcome. We find that CNA burden across the genome, defined as the percentage of the tumor genome affected by CNA, was associated with biochemical recurrence and metastasis after surgery in these two cohorts, independent of the prostate-specific antigen biomarker or Gleason grade, a major existing histopathological prognostic variable in prostate cancer. Moreover, CNA burden was associated with biochemical recurrence in intermediate-risk Gleason 7 prostate cancers, independent of prostate-specific antigen or nomogram score. We further demonstrate that CNA burden can be measured in diagnostic needle biopsies using low-input whole-genome sequencing, setting the stage for studies of prognostic impact in conservatively treated cohorts.

| S-EPMC4121784 | biostudies-literature

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