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

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

PROVIDER: PRJNA357064 | ENA |

REPOSITORIES: ENA

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

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 | 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 [Fig8b]

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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]

2016-12-13 | GSE92268 | 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:This SuperSeries is composed of the SubSeries listed below.

2016-12-13 | GSE92271 | GEO

Copy number alteration in Wilms' tumor with custom-designed miRNA probes

Project description:The aim of this study is to discover loss of specific miRNA loci in Wilms' tumors using array CGH. Custom arrays were designed based on the Agilent 2x105K Human Whole Genome Genomic microarray with Agilent’s eArray program (https://earray.chem.agilent.com/earray/), with additional probes that cover all miRNA regions (200 bps before, within and after each miRNA from miRBase v13, with each probe in triplicates to enhance the reliability). All custom-designed probes were designed in UCSC hg18. Probes from Agilent’s database were lifted-over from hg19 to hg18 (LiftOver tool: http://genome.ucsc.edu). The Agilent 2x105K custom-design whole genome microarray was used to analyze genomic alterations in Wilms' tumor samples compared to normal human genomic DNA (Promega p/n G1523).

2012-03-30 | E-GEOD-28397 | biostudies-arrayexpress

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-other

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