Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis of somatic copy number alterations and chromosomal breakages in osteosarcoma

ABSTRACT: Osteosarcoma (OS) is the most common primary malignant tumor of bone; it occurs most commonly in the metaphyseal regions of long bones in adolescents and young adults. Conventional osteosarcoma is characterized by complex karyotypes with a high degree of aneuploidy and numerous structural aberrations such as copy number alterations (CNAs) and genomic rearrangements. We characterized the landscape of somatic copy number alterations (SCNAs) in a large cohort (n=160) of osteosarcoma (OS) samples using the whole-genome CytoScan High Density arrays. This experiment is an extension of E-MTAB-3998. It contains data for 97 samples that is also included in E-MTAB-3998. The samples derived from E-MTAB-3998 identified using the 'Description' field in the sample attributes.

ORGANISM(S): Homo sapiens

SUBMITTER: Hongen Xu

PROVIDER: E-MTAB-4815 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix CytoscanHD Arrays of 113 Osteosarcoma Samples

Project description:Osteosarcoma (OS) is the most common primary malignant tumor of bone; it occurs most commonly in the metaphyseal regions of long bones in adolescents and young adults. Conventional osteosarcoma is characterized by complex karyotypes with a high degree of aneuploidy and numerous structural aberrations such as copy number alterations (CNAs) and genomic rearrangements. The data comprise of array copy number data (N=113) from pre-therapeutic osteosarcoma. These have been derived from Affymetrix CytoscanHD. The study searches for driver genes and examines cancer evolution. Note (added 8th June 2016): This experiment is extended in an experiment described under accession E-MTAB-4815. It contains data for 97 samples from this experiment are also included in E-MTAB-4815.

2015-11-09 | E-MTAB-3998 | biostudies-arrayexpress

Whole genome copy number profiles of FFPE samples from patients with metasatic colorectal cancer (mCRC)

Project description:Metastatic colorectal cancer (mCRC) is associated with multiple somatic copy number alterations (SCNAs). We analyzed SCNAs to estimate overall survival (OS) and progression free suvival (PFS) for mCRC patients treated with bevacizumab in combination with oxaliplatin or irinotecan.

2018-11-21 | GSE110785 | GEO

DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Affymetrix]

Project description:Metastatic urothelial carcinoma (UC) of the bladder is associated with multiple somatic copy number alterations (SCNAs). We evaluated SCNAs to identify predictors of poor survival in patients with metastatic UC treated with platinum chemotherapy. We obtained overall survival (OS) and DNA copy number data from UC patients in a Spanish discovery cohort and three validation cohorts. GISTIC was used to identify altered regions, and associations between copy number gains/losses and OS were determined by a Cox proportional hazard model adjusting for performance status and visceral disease The output files of the GISTIC 2.0 software are linked as supplementary files on Series record along with readme.txt file describing the contents of each file/column.

2013-07-07 | E-GEOD-39280 | biostudies-arrayexpress

DNA copy number gain at 1q23.3 is associated with poor survival in metastatic bladder cancer [Agilent]

2013-07-07 | E-GEOD-39281 | biostudies-arrayexpress

Genotyping by array of cartilage tumors taken from human patients

Project description:In this study, a series of 102 cartilage tumors was used to uncover the molecular diversity of chondrosarcomas through the profiling of mRNA, miRNA, DNA methylation, DNA copy number aberrations and point mutations. An integrated classification using multiple molecular dimensions revealed three major molecular features unraveling the diversity in clinical outcome of chondrosarcoma: a high mitotic state, regional 14q32 loss of expression and IDH mutations leading to genome-wide hypermethylation. These three robust and simple molecular features classify chondrosarcoma in subtypes with superior clinical value as compared to the current grading system.

2019-08-05 | E-MTAB-8213 | biostudies-arrayexpress

DNA copy number profiling of canine osteosarcoma

Project description:Identification of DNA copy number imbalances in 22 spontaneous canine osteosarcoma cases using array comparative genomic hybridization (aCGH) analysis

2013-11-01 | E-MTAB-1986 | biostudies-arrayexpress

Homo sapiens

Project description:TARGET: Osteosarcoma (OS)

| PRJNA89527 | ENA

Genomic heterogeneity of osteosarcoma - implementing order on the level of functional modules

Project description:Osteosarcoma (OS) represents the most common pediatric bone cancer with complex karyotypes. On the genomic level a highly variable degree of alterations in nearly all chromosomal regions and between individual tumors is observable. This hampers the identification of common drivers in OS biology. To identify these common molecular mechanisms involved in the maintenance of OS, we aimed to determine copy number associated gene networks to formalize the tumor heterogeneity between individual patients.

2014-10-31 | E-MTAB-3034 | biostudies-arrayexpress

Plasma profiling of miRNAs in mouse model of osteosarcoma.

Project description:Osteosarcoma (OS) is the primary bone tumor in children and young adults. Currently, there are no reliable, non-invasive biological markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from a genetically engineered mouse model of OS to identify a profile of four plasma miRNAs. Plasma from mice with OS were profiled for miRNAs and compared with the profile of plasma from disease-free mice

2015-01-24 | E-GEOD-65236 | biostudies-arrayexpress

Posterior Amorphous Corneal Dystrophy Is Associated with a Deletion of Small Leucine-rich Proteoglycans on Chromosome 12

Project description:Posterior amorphous corneal dystrophy (PACD) is a rare, autosomal dominant disorder affecting the cornea and iris. After next-generation sequencing of the family in which linkage analysis identified a chromosomal locus for PACD on 12q21.33 failed to yield a pathogenic mutation, array-based copy number analysis and qPCR detected a deletion on 12q21.33 containing four genes encoding small leucine-rich proteoglycans (SLRPs): KERA, LUM, DCN, and EPYC. Two other families with PACD also demonstrated deletion of these SLRPs, which together with murine models of KERA, LUM, and DCN deficiency provide convincing evidence that PACD is caused by haploinsufficiency of these SLRPs. Copy number analysis of 750K SNP and 1.9 non-polymorphic probes present on the Affymetrix CytoScan HD array. Samples were separated by affection status. Eight unaffected and 5 affected samples from across 3 families were analyzed. Analysis was performed using the Affymetrix Chromosome Analysis Suite (ChAS) v.2.0 software.

2014-06-04 | E-GEOD-50573 | 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