Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

95 Breast Cancer Exome Affymetrix SNP6 Array Data

ABSTRACT: A standard Affymetrix SNP6.0 assay was performed on the tumour samples of patients where we have exonic sequence data from both the tumour and normal DNA of the same patients. The resulting cellularity, copy number and ploidy information generated helped to inform bespoke algorithms in analysing the sequence data.

ORGANISM(S): Homo sapiens

DISEASE(S): invasive ductal carcinoma

SUBMITTER: Stuart McLaren

PROVIDER: E-MTAB-1110 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix SNP6 Array Data for 22 Adenoid Cystic Carcinoma samples also subjected to whole exome sequencing

Project description:A standard Affymetrix SNP6.0 assay was performed on the tumour samples of patients where we have exonic sequence data from both the tumour and normal DNA of the same patients. The resulting cellularity, copy number and ploidy information generated helped to inform bespoke algorithms in analysing the sequence data.

2013-06-01 | E-MTAB-1141 | biostudies-arrayexpress

Copy number variation comparison between control and CC214-2 resistant GBM39 xenografts

Project description:Here we present genome-wide copy number variation data on two vehicle treated and two CC214-2 (an mTOR kinase inhibitor) resistant GlioBlastoma Multiforme 39 (GBM39) xenografts, showing the absence of significant differences between the two groups, demonstrating that resistance to CC214-2 is due to adaptation rather than gene mutations. The genomic DNA extracted from the 4 xenografts samples was analysed with genome-wide Affymetrix SNP6.0 array

2013-12-06 | E-GEOD-53042 | biostudies-arrayexpress

Breast cancer SNP6 arrays_more

Project description:Affymetrix SNP6.0 array breast cancer data

| EGAD00010001079 | EGA

Identification of SNPs using genomic DNA and allele specific expression using nascent RNA on snp6 array

Project description:Disappearance of the Barr body has long been considered a hallmark of cancer, although whether this corresponds to epigenetic instability and transcriptional reactivation, or to genetic loss, has remained unclear. Here we show that in breast cancer cell lines as well as primary breast tumors, the inactive X chromosome frequently displays a highly abnormal 3D nuclear organization, with global perturbations in its characteristic heterochromatic state, including apparent gain of euchromatic marks and lessening of repressive marks such as H3K27me3 and promoter DNA methylation. Genome-wide profiling of chromatin and transcription reveal modified epigenomic landscapes in cancer cells accompanied by a significant degree of X-linked gene reactivation, affecting genes previously implicated in cancer, including the histone deacetylase, HDAC8 and transducin (Beta)-Like 1X-Linked, TBL1X. We provide proof of principle that epigenetic deregulation can indeed perturb the dosage of some X-linked factors and demonstrate that many of these genes are reactivated in primary breast tumors. Our study establishes that the inactive X is subject to epigenetic erosion in a cancer context and sets the stage for the use of chromatin marks and X- chromosome genes as potential biomarkers to assess epigenetic changes in cancer. Examination of allele specific expression of genes using nascent RNA on snp6 array by comparing it with snp6 results from genomic DNA.

2015-01-22 | E-GEOD-62965 | biostudies-arrayexpress

RNAseq of patients with Ewings sarcoma

Project description:Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewings sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings sarcoma tumours.

2016-05-18 | E-ERAD-65 | biostudies-arrayexpress

Clonal Selection Drives Genetic Divergence of Metastatic Medulloblastoma [Affymetrix SNP6 Arrays]

Project description:Medulloblastoma, the most common malignant pediatric brain tumour, disseminates by shedding cells into the cerebrospinal fluid, which then re-implant to cover the surface of the brain and spinal cord. Metastases are a very poor prognostic sign at presentation and are usually lethal at recurrence. Mechanisms driving dissemination have been described in the bulk primary tumour, with the underlying assumption that primary tumour and metastases are biologically similar. Here we show that in both mouse and human medulloblastoma, multiple metastases from a single animal are extremely similar, but are genetically highly divergent from the primary tumour. Clonal genetic events in the metastases can be demonstrated in a restricted sub-clone of the primary tumour, suggesting that only rare cells within the primary tumour have the ability to metastasize. Failure to account for the bicompartmental nature of primary and metastatic medulloblastoma represents a major barrier to the development of effective targeted therapies.

2011-12-09 | GSE34280 | GEO

ICGC breast cancer sequencing project SNP6 data

Project description:Affymetrix SNP6.0 breast cancer genome sequencing data

| EGAD00010000915 | EGA

Pharmacogenomics characterization of the MDM2 inhibitor MI-773 reveals candidate tumours and predictive biomarkers

Project description:Affymetrix SNP6.0 array data used to reveal predictive biomarkers of tumour sensitivity to MI-773 . MI-773 is a recently developed small-molecule inhibitor of the Mouse Double Minute 2 (MDM2) proto-oncogene. Here we report an integrative pharmacogenomic study to gain further insights into the therapeutic potential of the compound

2021-10-27 | GSE178763 | GEO

High-resolution genome-wide copy number analysis of low grade serous ovarian tumours

Project description:Integration of genomic copy number analysis (Affymetrix SNP6.0 arrays) and oncogenic RAS/RAF mutation status with clinical features and tumour progression. This study found that loss of the 9p and the CDKN2A locus with the most significantly enriched copy number aberration distinguishing serous border tumors from low grade serous carcinomas, suggesting this is a key step to tumor progression.

2015-03-01 | GSE58579 | GEO

Clonal Selection Drives Genetic Divergence of Metastatic Medulloblastoma [Affymetrix SNP6 Arrays]

2011-12-09 | E-GEOD-34280 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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