Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affymetrix OncoScan FFPE Array array data from Li-Fraumeni Syndrome tumors

ABSTRACT: Loss of heterzygosity in TP53 Affymetrix OncoScan FFPE arrays were performed according to the manufacturer's directions on DNA extracted from tumors Copy number analysis of Affymetrix OncoScan FFPE array was performed for two osteosarcoma lung metastases, one lung adenocarcinoma, one meningioma, one pleomorphic sarcoma

ORGANISM(S): Homo sapiens

SUBMITTER: Joshua Schiffman

PROVIDER: E-GEOD-64293 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix OncoScan FFPE Array array data from Li-Fraumeni Syndrome tumors

Project description:Loss of heterzygosity in TP53 Affymetrix OncoScan FFPE arrays were performed according to the manufacturer's directions on DNA extracted from tumors

2015-02-03 | GSE64293 | GEO

Oncoscan SNP-array analysis of DNA from esophageal samples of patients with Barrett's esophagus before and after progression to esophageal dysplasia and adenocarcinoma

Project description:The goal of this experiment is to characterize the copy number changes in esophageal mucosa of patients with Barrett's esophagus (BE) who progress to esophageal dysplasia and adenocarcinoma (BE progressors), as compared to patients with BE who do not progress for at least two years after esophageal mucosal sampling (non-progressors with never dysplastic Barrett's esophagus - NvDBE - samples). We sampled esophageal mucosa from the following groups: 1) non-dysplastic intestinal metaplasia from 16 patients at least 1 year before progression to esophageal dysplasia or adenocarcinoma (PP-BE); 2) non-dysplastic intestinal metaplasia from 21 patients who did not progress to dysplasia or adenocarcinoma for at least 2 years of surveillance after the tested sample (NvDBE) 3) non-dysplastic intestinal metaplasia from 21 patients who had temporally concurrent but spatially separate intestinal metaplasia samples from the same procedure (C-BE). 4) 10 samples of esophageal dysplasia or adenocarcinoma from patients in group 1 and 3. Samples were obtained by endoscopic biopsy, endomucosal resection or surgical resection, processed for clinical purposes by routine histopathologic methods, including formalin fixation and paraffin embedding (FFPE). DNA was extracted from 5 micro tissue sections of FFPE blocks and DNA extracted using QIAamp DNA FFPE Tissue Kit (Qiagen, Germantown, MD). Samples were processed for identification of somatic copy number alterations using the OncoScan FFPE Assay or the OncoScan CNV Assay (Affymetrix, Santa Clara, CA) according to the manufacturer's protocols. After hybridization, the arrays were washed, stained using GeneChip Fluidics Station 450 (Affymetrix) and scanned using GeneChip Scanner 3000 7G (Affymetrix). The CEL files generated are deposited here.

2019-10-27 | E-MTAB-7396 | biostudies-arrayexpress

Cross-laboratory validation of the OncoScan FFPE Assay, a multiplex tool for whole genome tumour profiling

Project description:162 FFPE samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan¬ FFPE assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations.

2015-02-18 | E-MTAB-2914 | biostudies-arrayexpress

Oncoscan™ Affymetrix array for pure LCIS, LCIS associated with ILC (invLCIS) and ILC

Project description:Oncoscan™ Affymetrix array was performed by Affymetrix using DNA extracted from macrodissected FFPE samples

2017-03-08 | GSE88909 | GEO

Analysis of whole-genome chromosomal alterations in primary cutaneous melanoma

Project description:In this experiment, FFPE samples of 41 primary cutaneous melanoma, 2 metastatic melanoma and 6 normal skin were used for DNA extraction and genotyping by Affymetrix OncoScan FFPE Assay, in order to define chromosomal alterations in copy number and loss of heterozygosity. Genomic damage was then correlated with clinical features of melanoma.

2015-11-01 | E-MTAB-3481 | biostudies-arrayexpress

Oncoscan for HER2 copy number assessment

Project description:Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues. Copy number analysis using Affymetrix Oncoscan arrays was performed for 29 primary breast cancers

2016-07-01 | E-GEOD-83916 | biostudies-arrayexpress

Oncoscan for HER2 copy number assessment

Project description:Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues.

2016-07-01 | GSE83916 | GEO

OncoScan Copy-Number Analysis of an Acute Panmyelosis with Myelofibrosis (APMF) Cohort

Project description:Affymetrix Oncoscan assays were performed according to the manufacturer's instructions from DNA extracted from FFPE tissues. Copy number analysis using Affymetrix Oncoscan arrays was performed for 16 APMF Samples.

2020-04-11 | E-MTAB-7888 | biostudies-arrayexpress

Genome-wide copy number alteration analysis to identify genetic signature for development of distant metastases in Papillary Thyroid Cancer

Project description:With the intent of identify alterations associated with the development of distant metastases in Papillary Thyroid Cancer (PTCs), we design a case-control study and performed genome-wide copy number variation analysis by Affymetrix Oncoscan FFPE Kit on 34 PTCs that developed distant metastases (DM-PTCs), 61 PTCs without distant metastases (CTRL-PTCs), and on 7 tissue from distant metastatic site

2018-03-01 | E-MTAB-5194 | biostudies-arrayexpress

Oncoscan for subclonal analysis in a lobular breast cancer with classical and solid growth pattern mimicking a solid-papillary carcinoma

Project description:Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast cancer tissues.

2017-02-09 | GSE94695 | GEO

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