Project description:Analysis of common pediatric osteosarcoma cell lines SaOS2, U2OS and 143B and two patient derived xenograft samples in comparison of osteoblast cell line hFOB1.19.

2022-02-22 | GSE197158 | GEO

Genome-wide gene expression analysis of high-grade osteosarcoma

Project description:We performed genome-wide gene expression data of high-grade osteosarcoma samples. In order to detect osteosarcoma drivers, we integrated these data with copy number data. We performed two different methods - a non-paired and a paired integrative analysis. Genome-wide gene expression analysis was performed on 84 pre-treatment high-grade osteosarcoma diagnostic biopsies, of which 29 overlapped with the 32 samples used for copy number analysis. Two different sets of control samples were used for comparison: osteoblasts (n=3) and mesenchymal stem cells (n=12, GEO accession number GSE28974).

2012-03-27 | E-GEOD-33382 | biostudies-arrayexpress

Genotyping by array of human pretherapeutic osteosarcoma from pediatric and adult patients.

Project description:Osteosarcoma pretherapeutic biopsy samples of pediatric and adult patients (median 14 years, mean 16.5) years were analyzed using Affymetrix 10K2 high-density SNP arrays. Numerical aberrations and allelic imbalances were correlated with the histological degree of necrosis and clinical follow-up.

2010-08-01 | E-MEXP-2688 | biostudies-arrayexpress

Copy number analysis of high-grade osteosarcoma

2012-03-28 | GSE33153 | GEO

Copy number analysis of high-grade osteosarcoma

Project description:We performed copy number analysis of high-grade osteosarcoma samples. in order to detect osteosarcoma drivers, we integrated these data with genome-wide gene expression data. We performed two different methods - a non-paired and a paired integrative analysis. Copy number analysis was performed on 32 pre-treatment high-grade osteosarcoma diagnostic biopsies, of which 29 overlapped with the 84 samples used for gene expression analyses.

2012-03-27 | E-GEOD-33153 | biostudies-arrayexpress

Genome-wide mRNA analysis substantiates high-grade central osteosarcoma cell lines and xenografts as representative for their originating primary tumor type

Project description:Conventional high-grade osteosarcoma is a primary malignant bone tumor, which is most prevalent in adolescence. Survival rates of osteosarcoma patients have not improved significantly in the last 25 years. Aiming to increase this survival rate, a variety of model systems are used to study osteosarcomagenesis and to test new therapeutic agents. Such model systems are typically generated from an osteosarcoma primary tumor, but undergo many changes due to culturing or interactions with a different host species, which may result into differences in gene expression between primary tumor cells, and tumor cells from the model system. We aimed to investigate whether gene expression profiles of osteosarcoma cell lines and xenografts are still comparable to those of the primary tumor. Osteosarcoma can be subdivided into several histological subtypes, of which osteoblastic, chondroblastic, and fibroblastic osteosarcoma are the most frequent ones. Using nearest shrunken centroids classification, we have generated an expression profile that can predict these histological subtypes in both osteosarcoma biopsies (n=66), as well as in two osteosarcoma model systems, i.e. osteosarcoma cell lines (n=13) and xenografts (n=18). Based on the preservation of mRNA expression profiles that are characteristic for the histological subtype we propose that these model systems are representative to the primary tumor from which they are derived.

2011-09-21 | GSE30699 | GEO

WGS and WES of pediatric osteosarcoma

Project description:Despite being the most common childhood bone tumor, the genomic characterization of osteosarcoma remains incomplete. Very few metastatic cases have been sequenced to date, a required step to better understand the progression and evolution of this tumor. Here, we present an integrative analysis of whole genome and whole exome sequencing (WGS and WES) of a cohort of primary and metastatic pediatric osteosarcoma, in order to identify recurrent genomic alterations between and within patients.

| EGAS00001003342 | EGA

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