Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Precursor lesions clonal architecture and relapse in Wilms nephroblastoma

ABSTRACT: Targeted resequencing at high depth (21 genes, 9 chromosomal regions): at least 4 FFPE samples per case and matched germline DNA: • 100 cases with detailed outcome data, including 15 cases with tumour relapse (515 samples) • 40 cases with matched pre-chemotherapy biopsies (240 samples) • 50 nephrogenic rests matched to above cases (50 samples) We expect a proportion (possibly 10%) of cases to be mutationally silent on the above studies, and propose to subsequently carry out integrated whole-genome, methylome and transcriptome studies on matched frozen tissue from these cases

PROVIDER: EGAS00001001422 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

EGAS00001001422-sc-20170309 - samples

Project description:Targeted resequencing at high depth (21 genes, 9 chromosomal regions): at least 4 FFPE samples per case and matched germline DNA: * 100 cases with detailed outcome data, including 15 cases with tumour relapse (515 samples) * 40 cases with matched pre-chemotherapy biopsies (240 samples) * 50 nephrogenic rests matched to above cases (50 samples) We expect a proportion (possibly 10%) of cases to be mutationally silent on the above studies, and propose to subsequently carry out integrated whole-genome, methylome and transcriptome studies on matched frozen tissue from these cases

| EGAD00001003217 | EGA

Comparison of gene expression in whole blood of mice subjected to normobaric hypoxia in vivo.

Project description:To determine hypoxia mediated changes in whole blood, normal C57Bl/10 mice were gradually exposed to a chronic hypoxic environment, equivalent to an altitude of 6500m, for 2 weeks in vivo. Control, age-matched mice were maintained under normoxic, normobaric conditions by exposing them to ambient air in Philadelphia (c. 50 mts above sea level).

2010-04-25 | GSE15894 | GEO

RNA sequencing of T-ALL (COG study)

Project description:The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure or relapse. We investigated 213 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL Studies 9404 and 0434 and identified a cluster cases characterized by increased expression of HOX9/10. In samples with >8-fold HOXA9/10 deregulation, the presence of specific molecular lesions were confirmed through a systematic review of cytogenetic databases, FISH and PCR testing. In cases with no identifiable lesions using the methods above, RNA sequencing was performed (Illumina and Ion Proton). Fifteen cases selected for RNA sequencing met three criteria: HOXA9/10 expression ≥8-fold above the median, sufficient RNA, and an incomplete or absent molecular explanation for each sample’s HOXA9/10 deregulation. Three cases were confirmed to have PICALM-AF10 fusions. Two additional AF10-R cases showed DDX3X-AF10 lesions, one of which harbored a novel CASK gene fragment in a complex CASK-DDX3X-AF10 translocation. Two cases harbored NUP98 fusions46 and one case each was identified for MLL-AF6, MLL-PICALM, HOXA10-(3’UTR)TRBC45, STAG2-LMO2, LOC338817-CCDC91. We could not identify fusion transcripts in 3 cases.

2017-06-29 | GSE71359 | GEO

Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer

Project description:Human salivary samples from reterospective and prospective cases of breast, prostate, and colon cancer cases along with matched controls.

| PRJEB56605 | ENA

Investigating stromal reprogramming in canine mammary adenoma using next-generation RNA sequencing of FFPE subsections

Project description:Cancer-associated stroma (CAS) and matched normal stroma (NS) samples from 13 cases of canine mammary adenoma

2020-04-06 | GSE135454 | GEO

Transcriptome Analysis Of Human Rett Syndrome Brain

Project description:Transcriptome analysis of postmortem brain samples frrom frontal and temporal cortex of Rett Syndrome cases and matched controls. These data identify genes differentially expressed in postmortem brain tissue from Rett Syndrome cases.

2015-11-24 | GSE75303 | GEO

Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma

Project description:Cancer-associated stroma (CAS) and matched normal stroma (NS) samples from 15 cases of canine mammary carcinoma (mCA).

2019-08-01 | GSE135183 | GEO

The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma

Project description:We analysed a cohort of breast papillary lesions cases with (n=4) or without (n=7) co-existed cancer for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included pure papilloma (withoout cancer) (n=7), papilloma cases synchronous with cancer (n=4). We have analysed copy number calling from these samples including carcinoma components of synchronous cases in order to understand the precursor relationship as well any biomarker for progression from papillary lesions to carcinoma.

2020-01-29 | GSE131087 | GEO

Epigenome analysis of precursor lesions of endometrial endometrioid carcinoma

Project description:We performed genome-wide DNA methylation profiling on 126 samples from 59 cases with atypical endometrial hyperplasia, atypical polypoid adenomyoma, and endometrial carcinoma, all of whom had received oral MPA treatment at the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

2026-04-30 | GSE299925 | GEO

miRNA Expression Profiles of Premalignant and Malignant Arsenic-Induced Skin Lesions

Project description:Total RNA was purified from keratinocytes isolated from FFPE arsenic-induced skin lesion samples collected from individuals exposed to high concentrations of arsenic exceeding 50 ppb in drinking water in Murshidibad district of West Bengal, India.

2018-06-01 | GSE102892 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data