Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affymetrix SNP6.0 on Ollier disease-related tumors

ABSTRACT: Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22984 | GEO | 2011/08/26

SECONDARY ACCESSION(S): PRJNA129151

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Affymetrix SNP6.0 on Ollier disease-related tumors

Project description:Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors. To understand the genetic mechanism behind the development of enchondroma, we mainly focus on enchondromas and found alterations were validated. We used 14 enchondromas and 23 chondrosarcomas of 28 Ollier patients. We also used 30 controls (blood, saliva or frozen tissue). As controls, normal DNA derived from fresh frozen muscle tissue (n=3), peripheral blood lymphocytes (n=4) or saliva (n=4) was available for 11 Ollier patients and 3 patients with unrelated bone diseases. We used blood lymphocyte DNA from 12 healthy controls and 1 HapMap sample. We also isolated DNA from saliva for 3 of these controls to validate the use of saliva DNA in this study.

2011-08-26 | E-GEOD-22984 | biostudies-arrayexpress

Expression array using Maffucci tumours

Project description:We did whole genome analysis of enchondromas and chondrosarcomas of Maffucci patients. Since the disease is very rare, we had only three frozen tumour samples were available to continue with the expression array. Enchondromas of Maffucci syndrome did not show any loss of heterozygosity (LOH) or common copy number alterations (CNA) and we looked at the differentially expressed genes between Ollier high grade and Maffucci high grade tumours. There were no significant differentially expressed genes were found between these two groups. This might be due to the small sample size. We used Affymetrix SNP 6.0 array on enchondromas (n=4) and chondrosarcomas (n=2) and compared the results to a previously studied cohort of patients with Ollier disease (n = 37). We used Illumina expression array v3 chip on enchondroma (n=1) and chondrosarcomas (n=2) from Maffucci patients.

2011-07-18 | E-GEOD-26667 | biostudies-arrayexpress

Affymetrix SNP6.0 array data for PAX5 amplified acute lymphoblastic leukemia

Project description:Intragenic PAX5 amplification in <1%of B-cell precursor acute lymphoblastic leukaemia. Affymetrix SNP 6.0 array analysis was undertaken in patients who showed amplication of PAX5 by MLPA testing using the P335-IKZF1 MLPA kit (www.mlpa.com, MRC Holland, The Netherlands)

2017-06-09 | GSE99813 | GEO

Affymetrix SNP6.0 array data for EBF1-PDGFRB rearranged acute lymphoblastic leukemia

Project description:The EBF1-PDGFRB gene fusion accounts for <1% B-cell precursor acute lymphoblastic leukaemia and occurs within the Philadelphia-like ALL subtype. We performed Affymetrix SNP 6.0 array was undertaken patients who tested positive for EBF1-PDGFRB rearrangement by FISH and/or RT-PCR.

2016-04-05 | GSE77557 | GEO

germline_2 SNP6.0

Project description:Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array

| EGAD00010001813 | EGA

leukemia SNP6.0

Project description:Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array

| EGAD00010001637 | EGA

germline SNP6.0

Project description:Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array

| EGAD00010001635 | EGA

leukemia_2 SNP6.0

Project description:Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array

| EGAD00010001814 | EGA

Affymetrix SNP 6.0 array data for chordoma samples

Project description:Chordomas are rare, low to intermediate grade malignant bone tumors of the axial skeleton, believed to originate from the notochord. Treatment options are limited and mainly restricted to surgical excision, as chordomas have been proven to be largely resistant to conventional ionizing radiation and chemotherapy. Therefore a new cell line was established. The cell line has been characterized by immunohistochemistry,western blot and karyotyping using cobra fish technology. Copy number variations (CNV) and loss-of heterozygosity (LOH) from fibroblasts, tumor tissue, low and high cell line passage was evaluted by using Affymetrix 6.0SNP Arrays. DNA isolated from the patients MNCs was used as control. The cell line MUG-Chor1 is highly similar to genetic profiles of chordomas and provides therefore a powerful tool for further investigations. Affymetrix SNP 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryo material or cell lines. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 samples. 60 samples from HapMap database were used as references for copy number inference.

2012-07-11 | E-GEOD-25720 | biostudies-arrayexpress

Genotyping by array of human primary acute myeloid leukemia cells on the Affymetrix 6.0 SNP array to evaluate prognostic relevance

Project description:DNA copy number, and LOH using a large set of paired samples (n=108+11), i.e. AML cells at diagnosis and normal leukocytes at remission. Affymetrix 6.0 SNP array were used.

2016-11-02 | E-MTAB-1586 | biostudies-arrayexpress