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Ena-DATASET-VUMC-CCA-28-02-2018-15:43:22:599-948 - samples

ABSTRACT: Shallow sequencing of metastatic colorectal cancer samples for the Angiopredict and Nobev cohorts described in: van Dijk et al., JCO, in revision

PROVIDER: EGAD00001003990 | EGA |

REPOSITORIES: EGA

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VUMC-CCA

Project description:Organisation EGAO00000000195

| EGAO00000000195 | EGA

Expression analysis of Yersinia intermedia strain ATCC 29909 at 28 C in minimal medium with glucose under aerobic and anaerobic conditions

Project description:Investigation of whole genome gene expression level changes in Yersinia intermedia strain ATCC 29909 in response to oxygen. The experiments and results have not been published yet (manuscript has been submitted to journal office and is under revision)

2013-08-21 | GSE50043 | GEO

ena-DATASET-VUMC-CCA-30-11-2021-13:35:58:790-356 - samples

Project description:Shallow whole genome sequencing and targeted sequencing of DLBCL patients treated in the HOVON84 trial

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ena-DATASET-VUMC-CCA-30-11-2021-10:54:57:998-350 - samples

Project description:Shallow whole genome sequencing and targeted sequencing of DLBCL patients treated in the PETAL trial

| EGAD00001008386 | EGA

A transcriptional program for arbuscule degeneration during AM symbiosis is regulated by MYB1

Project description:The array experiment compares gene expression in roots of Medicago truncatula A17 and Medicago truncatula mutant mtpt4-1 colonized with Gigaspora gigantea. This experiment enabled the identification of a plant transcriptional program associated with arbuscule degeneration. The experiment and data are described in Floss et al., Current Biology (in revision).

2017-04-07 | GSE95545 | GEO

ena-DATASET-VUMC-CCA-12-10-2016-16:43:39:044-188 - samples

Project description:Background: In follicular lymphoma (FL), studies addressing the prognostic value of microenvironment-related immunohistochemical (IHC) markers and tumor cell-related genetic markers have yielded conflicting results, precluding implementation in practice. Therefore, the Lunenburg Lymphoma Biomarker Consortium (LLBC) performed a validation study for published markers. Methods: To maximize sensitivity, an end-of-spectrum design was applied for 122 uniformly immunochemotherapy-treated FL patients retrieved from international trials and registries; early failure (EF): progression or lymphoma-related death <2 years versus long remission: response duration of >5 years. IHC staining for T-cells and macrophages was performed on tissue microarrays from initial biopsy and scored with a validated computer-assisted protocol. Shallow whole-genome and deep targeted sequencing was performed on the same samples. Results: 96/122 cases with complete molecular and immunohistochemical data were included in the analysis. EZH2 wild-type (p=0.006), gain of chromosome 18 (p=0.002), low percentages of CD8+ cells (p=0.011) and CD163+ areas (p=0.038) were associated with EF. No significant differences in other markers were observed, thereby refuting previous claims on their prognostic significance. Conclusion: Using an optimized study design, this LLBC study validates wild-type EZH2 status, gain of chromosome 18, low percentages of CD8+ cells and CD163+ area as predictors of EF to immunochemotherapy in FL.

| EGAD00001002738 | EGA

ena-DATASET-VUMC-CCA-30-11-2021-09:00:06:153-347 - samples

Project description:Stage I and stage III/IV Follicular lymphoma samples, shallow whole genome sequencing for copy number analysis and targeted capture sequencing for mutation and translocation analysis.

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ena-DATASET-VUMC-CCA-30-11-2021-11:10:02:536-351 - samples

Project description:Shallow whole genome sequencing for copy number analysis and targeted capture sequencing data for translocation and mutation anslysis of paired primary and relapse PCNSL and PTL samples

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VUmc - CCA Genome Core

Project description:Organisation EGAO00000000238

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ena-DATASET-VUMC-CCA-09-10-2020-14:30:07:774-77 - samples

Project description:Shallow whole genome sequencing of 29 BIA-ALCL patients for copy number analysis and 24 Alk-negative ALCL samples as control cohort. 7 Whole exome sequencing BIA-ALCL samples.

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