Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome SNP array data from myelodysplastic syndromes (MDS) patients

ABSTRACT: With the whole genome SNP array information obtained from tumor and matched normal control, we could evaluate the acquired copy number variations (CNVs) and uniparental disomies (UPDs) . Seven MDS patients in a whole genome sequencing project were included in this experiment.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57229 | GEO | 2014/05/22

SECONDARY ACCESSION(S): PRJNA246092

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Whole genome SNP array data from myelodysplastic syndromes (MDS) patients

Project description:With the whole genome SNP array information obtained from tumor and matched normal control, we could evaluate the acquired copy number variations (CNVs) and uniparental disomies (UPDs) . Seven MDS patients in a whole genome sequencing project were included in this experiment. To detect acquired CNVs and UPDs in MDS patients, we genotyped both CD34+ cell from bone marrow and matched skin tissue.

2014-05-22 | E-GEOD-57229 | biostudies-arrayexpress

Affymetrix SNP array data for myelodysplastic syndromes (MDS) samples

Project description:The progressive mechanism of myelodysplastic syndrome (MDS) remains unknown. We report that ROBO1 and ROBO2 are identified as novel progression-related somatic mutations using whole-exome and targeted sequencing in six of 16 (37.5%) paired MDS patients undergoing disease progression. To investigated the effect of ROBO1 or ROBO2 on ROBO1/2 CN number and LOH, we employed a Cytosan 750K chip to analyze the copy-number variations (CNVs) and loss of heterogeneity (LOH) in MDS patients with ROBO1&2 mutations. Copy number and LOH analysis of Affymetrix CytoScan 750K array was performed for 14 MDS patients with ROBO1 or ROBO2 mutations

2015-09-15 | E-GEOD-73005 | biostudies-arrayexpress

Affymetrix SNP array data for myelodysplastic syndromes (MDS) samples

2015-09-15 | GSE73005 | GEO

Affymetrix SNP array data for myelodysplastic syndromes (MDS) and related neoplasms

Project description:In this study, to obtain a complete registry of genetic lesions in MDS and to identify novel therapeutic targets, we performed SNP array analysis and whole exome analysis for novel mutations using high-throughput sequencing technologies. In whole exome analysis, paired CD3-positive T cells were used as a normal control. By comparing sequences in tumors and paired T cells, 268 non-synonymous somatic mutations were confirmed with an overall true positive rate of 53.9 %, including 206 missense, 25 nonsense, and 10 splice site mutations, and 27 frameshift-causing insertions/deletions (indels). The mutations of the known gene targets, however, accounted for only 12.3 % of all detected mutations (N = 33), and the remaining 235 mutations involved previously unreported genes. Combined with the genomic copy number profile obtained by SNP array karyotyping, this array of somatic mutations provided a landscape of myelodysplasia genomes. Copy number analysis of Affymetrix 250K SNP arrays was performed for 29 MDS or related neoplasms and paired 29 germline samples.

2011-09-11 | E-GEOD-31174 | biostudies-arrayexpress

Exome sequencing identifies somatic mutations of DDX3X in natural killer/T-cell lymphoma

Project description:With the whole genome SNP array information obtained from tumor and matched normal control, we could evaluate the acquired copy number alterations (CNAs) and uniparental disomies (UPDs) . Here we identified somatic mutations by whole-exome sequencing in 25 NKTCL patients and extended validation through targeted sequencing in an additional 80 cases.

2015-05-29 | GSE69382 | GEO

Affymetrix SNP array data for acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS)

Project description:We recently identified recurrent mutations of cohesin complex in myeloid neoplasms through whole-exome sequencing analysis. In this study, we performed SNP array analysis to detect abnormal copy number of the cohesin genes. Copy number analysis by Affymetrix 50K or 250K SNP arrays was performed for 93 AML and 70 MDS tumor samples.

2013-07-16 | E-GEOD-47682 | biostudies-arrayexpress

Affymetrix SNP array data for myelodysplastic syndromes (MDS) and related neoplasms

2011-09-12 | GSE31174 | GEO

Myelodysplastic Syndromes (MDS) and Acute Myeloid Leukaemia (AML)

Project description:A 10K cDNA microarray was used to compare neutrophil RNA from 21 MDS patient and 2 AML patients to pooled neutrophil RNA from 7 healthy controls.

2005-01-09 | E-GEOD-971 | biostudies-arrayexpress

Affymetrix SNP array data for dic(1;7)(q10;p10) in Myelodysplastic Syndromes (MDS)

Project description:The unbalanced translocation t(1;7)(q10;p10), generating 1q trisomy and 7q monosomy, is due to centromere-centromere juxtaposition. This dicentric chromosome is a recurrent change in myelodysplastic syndromes (MDS), with half the cases arising after chemo/radio-therapy. To date, given the absence of genes within the centromeric regions, no specific molecular events have been identified in this cytogenetic subgroup. We first identified a comprehensive genetic and epigenetic landscape of MDS with dic(1;7)(q10;p10) and compared it to normal controls and other therapy-related Myeloid Neoplasms (t-MNs). RNA-seq showed a unique downregulated signature in dic(1;7) cases, affecting more than 80% of differentially expressed genes. As revealed by pathway and gene ontology analyses, downregulation of ATP-binding cassette (ABC) transporters and of genes related to lipid metabolism, and upregulation of p53 signaling were the most relevant biological features of dicentric-positive MDS. Despite 1q trisomy, more than 50% of 1q deregulated genes were downregulated. This partial gene dosage effect was clarified by epigenetic analysis, which highlighted the presence of a specific hypermethylated pattern on 1q. Furthermore, in a supervised analysis, hypermethylation in all dicentrics clustered at intronic enhancers and was enriched for Krüppel-like transcription factors binding sites. Low expression levels of enhancer putative target genes accounted for more than 30% of the downregulated signature. Our findings demonstrate that alteration of centromeric DNA in dic(1;7) cases imposes a specific transcriptional program, driven by a unique epigenomic signature.

2019-09-01 | GSE118477 | GEO

Oxidative stress in myelodysplastic syndromes

Project description:Control of oxidative stress in the bone marrow (BM) is key for maintaining the balance between self-renewal, proliferation, and differentiation of hematopoietic cells. Breakdown of this regulation can lead to diseases characterized by BM failure such as the myelodysplastic syndromes (MDS). To better understand the role of oxidative stress in MDS development, we compared protein carbonylation as an oxidative stress marker in BM of patients with MDS and control subjects, and also patients with MDS under treatment with the iron chelator deferasirox.

2019-10-30 | PXD013609 | Pride

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