Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Osteosarcoma Genome-wide Association Study

ABSTRACT:

This is a genome-wide association study (GWAS) of osteosarcoma, the most common primary bone malignancy. Osteosarcoma typically occurs in adolescents and young adults. It occurs at increased frequency in several inherited cancer predisposition syndromes but the genetic contribution to sporadic osteosarcoma is largely unexplored. The objective of this study was to identify genetic risk factors for osteosarcoma by conducting a genome-wide association study.

We developed collaborations with multiple institutions in order to attain the necessary sample size required to discover novel loci in the genome associated with osteosarcoma using the GWAS approach. Genomic DNA (either blood or buccal in source) derived from osteosarcoma cases was obtained from each participating institution or research group.

De-identified blood or buccal cell DNA samples from osteosarcoma cases were derived from existing biobanks at the collaborative institutions. Control subjects were derived from existing NCI cohorts and matched by gender and ethnicity.

PROVIDER: phs000734 | dbGaP |

SECONDARY ACCESSION(S): PRJNA189539PRJNA189540

REPOSITORIES: dbGaP

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	GapExchange_phs000734.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs000734.OsteosarcomaRisk.v1.p1.MULTI.pdf	Pdf
	manifest_phs000734.OsteosarcomaRisk.v1.p1.c1.GRU.pdf	Pdf
	datadict_v2.xsl	Other

Items per page:

1 - 5 of 15

Similar Datasets

Blood samples as a surrogate of brain methylation

Project description:Epigenomic landscapes are variable between cells and tissue types and, fluctuate in time according to a number of factors such as the age related, environmental or nutritional factors among others. Existing biobanks that archive longitudinally assessed and correctly phenotyped samples have not stored exposure-disease relevant target tissue but DNA from peripheral sources such as the whole blood or buccal cells. Thus, a key question for the current epigenetic studies concerns the degree to which easily accessible peripheral tissues (such as blood) can be used to ask questions about the epigenomic changes taking place in inaccessible tissues such as the brain. In the current study we have compared the methylation profiles in brain (cortex and hippocampus) and blood samples within the same individuals in order to create an inventory of epigenetic marks for which measurements in blood are informative for the brain tissue.

2017-06-01 | GSE57300 | GEO

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

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

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. 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.

2017-06-02 | E-MTAB-4815 | biostudies-arrayexpress

Homo sapiens

Project description:A Genome-wide Association Study (GWAS) of Risk for Osteosarcoma

| PRJNA189540 | ENA

Homo sapiens

Project description:A Genome-wide Association Study (GWAS) of Risk for Osteosarcoma

| PRJNA189539 | ENA

plasma-derived exosomes from healthy and osteosarcoma

Project description:Identification of proteins from plasma-derived exosomes of from healthy controls and osteosarcoma patients by LC-MS/MS in label-free quantification.

2021-07-02 | PXD024072 | Pride

Canine osteosarcoma cell lines and tissues

Project description:Cell lines and tumor tissues from canine osteosarcomas with accompanying survival and breed data. Comparisons of gene expression between osteosarcoma-derived cell lines and osteosarcoma tissues.

2011-09-07 | E-GEOD-27217 | biostudies-arrayexpress

Gene expression profiling of thawing renal tissue.

Project description:Some biosamples obtained from biobanks may go through thawing before processing. We aim to evaluate the effects of thawing at room temperature for different time periods on gene expression analysis.

2014-05-05 | E-MTAB-2169 | biostudies-arrayexpress

Project description:Smithsonian Institution DNA Barcoding Network

| PRJNA81359 | ENA

Development of an osteosarcoma model with MYCN amplification and TP53 mutation in hiPS cell-derived neural crest cells

Project description:Osteosarcoma, derived from mesenchymal stem cells or osteoblasts, is the most common malignant bone tumor and the highly metastatic malignant phenotypes often with poor prognosis are related to modulation of TP53- and cell cycle-related pathways. MYC, which regulates the transcription of cell-cycle modulating genes, e.g. CCNE1, is used as a representative prognostic marker. MYCN, a member of MYC oncoprotein family, is highly expressed in a subset of osteosarcoma, however, its roles in osteosarcoma have not been elucidated extensively. Here, we attempted to make an in vitro tumorigenesis model by using hiPSCs derived neural crest cells, which is a precursor cell of mesenchymal stem cells, by MYCN overexpression in the background of heterozygousTP53 hotspot mutation (c.733G>A; p.G245S). MYCN-expressing transformed clones with TP53 mutation were isolated by soft agar colony formation, and injected subcutaneously and into periadrenal adipose tissue of immune-deficient mice, resulted in development of chondroblastic osteosarcoma. MYCN suppression decreased proliferation in MYCN-induced osteosarcoma cells, suggesting that MYCN seems to be one of the targets of osteosarcoma treatment. Further, comprehensive analysis of gene expression and exome sequencing of the MYCN-induced transformed clones indicated molecular context of osteosarcoma-specific feature such as activation of TGF-β signaling and DNA copy number amplification of GLI1. The model of MYCN-expressing chondroblastic osteosarcoma was developed from hiPSC-based neural crest cells, allowing us to provide useful tool for development of new tumor models using hiPSC-derived progenitor cells with gene modification and in vitro transformation.

2023-04-23 | GSE201511 | GEO