Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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

ORGANISM(S): Homo sapiens

SUBMITTER: Federica Torricelli

PROVIDER: E-MTAB-5194 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

Combination of multiomics approach and BCR-ABL based molecular testing: A better way to monitor treatment regimen and disease progression in Chronic Myeloid Leukemia [OncoScan]

Project description:We screened TKI-treated-CML-samples in different-phases based on < or >10% copies of BCR-ABL, undetected and control-samples for generating transcriptomics-profile. Transcriptionally, three clusters were identified which showed correlation with BCR-ABL transcript-levels i.e. <10% copies (I-cluster) , undetectable (II-cluster) and >10% copies (III-cluster). CML-new cases as well as Tyrosiine kinase treated-different phases of CML

2016-02-06 | E-GEOD-77571 | biostudies-arrayexpress

Combination of multiomics approach and BCR-ABL based molecular testing: A better way to monitor treatment regimen and disease progression in Chronic Myeloid Leukemia

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-02-05 | E-GEOD-77573 | biostudies-arrayexpress

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 Copy number analysis of Affymetrix OncoScan FFPE array was performed for two osteosarcoma lung metastases, one lung adenocarcinoma, one meningioma, one pleomorphic sarcoma

2015-02-03 | E-GEOD-64293 | biostudies-arrayexpress

Integrated Copy Number Analysis of Epstein Barr Virus (EBV)-Positive Diffuse Large B-Cell Lymphoma (DLBCL)

Project description:Copy number analysis was performed on EBV+ DLBCL samples compared with EBV- DLBCL. We analyzed the genomic DNA from 18 cases of EBV+ DLBCL, 21 cases of EBV- DLBCL, and 13 cases of nonneoplastic tonsillar tissues using OncoScan FFPE Express 2.0 (MIP). No technical replication were done.

2014-02-01 | E-MTAB-1971 | biostudies-arrayexpress

Transcription profiling of effect of hypoxia in human primary monocytes

Project description:Experiment with 6 hybridizations, using 30 samples of species [Homo sapiens], using 6 arrays of array design [Affymetrix GeneChip Human Genome HG-U133A [HG-U133A]], producing 6 raw data files and 6 transformed and/or normalized data files.

2005-10-10 | E-MEXP-445 | biostudies-arrayexpress

Copy number analysis of Gestational Trophoblastic Disease

Project description:Purpose was to determine whether varying gestational trophoblastic disease samples carry common copy number changes.

2021-04-14 | E-MTAB-10303 | biostudies-arrayexpress

WG-DASL expression profiling of formalin-fixed paraffin embedded primary breast tumours and matched lymph node metastases across four clinically relevant metastatic groups

Project description:The development of metastases is a complex multi-step process manifested by diverse patterns, involving single or multiple organs and different time-courses of distant recurrences. The aim of this study was to characterise molecular patterns associated with patterns of organ-specific metastatic spread observed in the clinic from FFPE embedded breast carcinomas and lymph node metastases. This study includes patients with four patterns of first metastatic sites: bone only (with no visceral metastases within 6 months of first metastasis); to viscera only (with no bone metastasis within 6 months of first metastasis); to bone and visceral organs within a 6 month period; and no recorded distant metastasis. The study population was composed of 5,061 patients diagnosed with invasive primary breast cancer without distant metastasis at the time of diagnosis between 1975 and 2005 from Guyâs Hospital. From the study population, an incidence-based case-control design was used to include patients from each of the metastatic groups and a control series randomly matched to cases according to having no reported metastasis up to the calendar date of metastasis. The aim of this expression profiling study was to characterise any molecular patterns that may be associated with the organ-specific metastatic spread observed in the clinic from FFPE embedded breast carcinomas and lymph node metastases.

2017-12-01 | E-MTAB-4003 | biostudies-arrayexpress

Liver tumor/normal pairs

Project description:A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quality CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA. Tumor FFPE were analyzed using matched normal FFPE as the reference. Tumor and normal pairs: 01-02, 12-13, 16-17, 08-09, 20-21, 24-25, 28-29, and 35-36. Tumor 32 has no matched normal sample.

2009-01-22 | E-GEOD-14353 | biostudies-arrayexpress

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