Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affymetrix SNP6.0 array for comparison of lung tumor and adjacent normal to high-throughput sequencing data

ABSTRACT: One lung tumor and its adjacent normal were profiled for copy-number alterations with the high-resolution Affymetrix SNP6.0 Array. The SRA ID for the high throughput sequencing project will accompany our study is SRP002045.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20584 | GEO | 2010/05/27

SECONDARY ACCESSION(S): PRJNA129855

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix SNP6.0 array for comparison of lung tumor and adjacent normal to high-throughput sequencing data

Project description:One lung tumor and its adjacent normal were profiled for copy-number alterations with the high-resolution Affymetrix SNP6.0 Array. The SRA ID for the high throughput sequencing project will accompany our study is SRP002045. One lung tumor sample and an adjacent normal sample were assayed on the Affymetrix SNP6.0 array.

2010-06-09 | E-GEOD-20584 | biostudies-arrayexpress

Performance Comparison of the Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-genome Microarrays in Complex Cancer Samples

Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This SuperSeries is composed of the SubSeries listed below.

2012-11-26 | GSE37979 | GEO

SNP6.0 copy number analysis of eight diffuse large B-cell samples and one matched blood sample

Project description:We performed a comparison analysis of the Affymetrix arrays SNP6.0 genome wide array (SNP6.0) and cytogenetic 2.7M whole-genome array (Cyto2.7M) using nine human samples. We compared the two array types with respect to four parameters including the size and breakpoints of the alterations detected, the actual CN assigned to the CNVs as well as long stretches of loss of heterozygosity. Overall, we found very good consistency between the two types of array on all parameters compared, even in regions with very complex changes. This GEO submission contains the SNP6.0 data. GEO submission, GSE37978 contains the Cyto2.7M data.

2012-11-26 | GSE37977 | GEO

Affymetrix SNP6.0 array data for different clinical outcomes of HBV infection

Project description:Chronic hepatitis B virus (HBV) infection is a serious global public health problem. To identify susceptibility loci for disease progression of HBV infection, we performed this genome-wide association study using DNA pools of case and control constructed by progressed HBV carriers (acute liver failure, liver cirrhosis, hepatocellular carcinoma) and asymptomatic HBV carriers separately. Performing GWAS on pools of DNA samples is an effective strategy to reduce the costs of studies and pooling DNA has been shown to be an efficient method to select candidate susceptibility loci for follow-up by individual genotyping. Affymetrix Genome-Wide Human Mapping SNP6.0 Arrays were performed for DNA pools, which were constructed by pooling 120 ng DNA from each participant. Four independent pools were created: case A was acute liver failure group (n = 86), case B was liver cirrhosis group (n = 88), case C was hepatocellular carcinoma group (n = 90) and case D was asymptomatic HBV carriers (n = 66) that was considered as control. Twelve chips (each pool was replicated in triplicate) were finished according to the manufacturer's instruction.

2013-12-10 | E-GEOD-26034 | biostudies-arrayexpress

Gene Expression and HD-SNP6.0 data from Primary Testicular (PTL), Primary Central Nervous System Lymphoma (PCNSL) and Primary Mediastinal B-cell Lymphoma (PMLBCL)

Project description:We obtained gene expression data and HD-SNP6.0 copy number data from PTL, PCNSL and PMLBCL samples and performed an integrative analysis on them. RNA was whole genome amplified using Nugen.

2015-12-31 | GSE61578 | GEO

Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.

Project description: Not available

| S-EPMC2806376 | biostudies-literature

Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays.

Project description: Not available

| S-EPMC2871725 | biostudies-literature

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

Project description:This SuperSeries is composed of the following subset Series: GSE20574: Agilent 244A aCGH array for comparison of lung tumor CNA to high-throughput sequencing data GSE20578: Assessment of mutation on expression levels GSE20584: Affymetrix SNP6.0 array for comparison of lung tumor and adjacent normal to high-throughput sequencing data Refer to individual Series

2010-05-27 | E-GEOD-20585 | biostudies-arrayexpress

Affymetrix SNP6.0 microarray data - Myelodysplastic syndromes

Project description:Mutations in the TET2 gene are frequent in myeloid disease, although their biological and prognostic significance remains unclear. We analyzed 355 patients with myelodysplastic syndromes using ‘Next-Generation’ sequencing (NGS) for TET2 aberrations; 91 of whom were also subjected to SNP6 array karyotyping. Seventy-one TET2 mutations, with a relative mutation abundance (RMA) ≥10%, were identified in 39 of 320 (12%) MDS and 16 of 35 (46%) CMML patients (p<0.001). Interestingly, 4 patients had multiple mutations likely to exist as independent clones or on alternate alleles, suggestive of clonal evolution. ‘Deeper’ sequencing of 96 patient samples identified 4 additional mutations (RMA 3%-6.3%). Importantly, TET2 mutant clones were also found in T cells in addition to CD34+ and total bone-marrow cells (23.5%, 38.5% and 43% RMA respectively). Only 20% of the TET2-mutated patients showed loss of heterozygosity at the TET2 locus. There was no difference in the frequency of genome-wide aberrations, TET2 expression or the JAK2V617F 46/1 haplotype between TET2-mutated and non-mutated patients. There was no significant prognostic association between TET2 mutations and WHO subtypes, IPSS score, cytogenetic status, or transformation to AML. On multivariate analysis, age (>50yrs) was associated with a higher incidence of TET2 mutation (p=0.02).

2010-07-30 | GSE23300 | GEO

RNA sequencing for cancer tissues and adjacent tissues of third-stage rectal cancer patients with and without blood vascular thrombus

Project description:The Agilent Human Gene Expression(8*60K，Design ID：039494) was used in this experiment of sequencing of the 12 samples. A total of 12 tissues were sequenced from adjacent and cancerous tissues of 6 patients with TNM stage 3 colon cancer. Three patients had cancer thrombus and three patients had no cancer thrombus.

2021-02-23 | GSE127069 | 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