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An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: allelic status

ABSTRACT: dChip analysis of 9 breast cancer cell lines. Data obtained from caBIG Part of a multi-dimensional analysis of gene copy number, allelic status, DNA methylation and gene expression data

ORGANISM(S): Homo sapiens

SUBMITTER: Raj Chari

PROVIDER: E-GEOD-21347 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

Project description:This SuperSeries is composed of the following subset Series: GSE17768: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: gene expression GSE17769: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: DNA methylation GSE21347: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: allelic status GSE21540: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: CGH Refer to individual Series

2010-12-31 | E-GEOD-21541 | biostudies-arrayexpress

SNP array analysis on Maffucci tumours

Project description:Here we have used four enchondromas and two chondrosarcomas of Maffucci patients. We also had one normal sample available for paired analysis in one of the chondrosarcoma II. We did not find any LOH or coomon copy number variation in all Maffucci enchondromas while chondrosarcomas are genetically unstable. Affymetrix SNP 6.0 array was performed using 4 EC and 2CS of Maffucci patients. Illumina expression v3 array was possible to perform using only 1 EC and 2 CS due to rarity of the disease. For SNP array, we used 29 control samples submitted previously (GSE22965) to creat baseline.

2011-07-18 | E-GEOD-26674 | biostudies-arrayexpress

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

Hodgkin lymphoma

Project description:This SuperSeries is composed of the following subset Series: GSE25986: Gene expression profiling of cell lines derived from classical Hodgkin lymphoma GSE25987: Gene expression profiling of Hodgkin lymphoma cell line KMH2: Comparison of CIITA-BX648577 knockdown cultures with non-silencing controls GSE25989: Copy number analysis of Hodgkin lymphoma cell lines KM-H2 and L-428 Refer to individual Series *** This submission represents the microarray gene expression and microarray copy number components of the study

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Profiles of genomic instability in high-grade serous ovarian cancer (HGSC) predict treatment outcome

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Maffucci tumours

Project description:This SuperSeries is composed of the following subset Series: GSE26667: Expression array using Maffucci tumours GSE26674: SNP array analysis on Maffucci tumours Refer to individual Series

2011-07-18 | E-GEOD-26675 | biostudies-arrayexpress

Profiling of differential allelic expression in horse, donkey, mule, and hinny placental tissues.

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2012-05-29 | E-GEOD-36352 | biostudies-arrayexpress

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: allelic status

Project description:dChip analysis of 9 breast cancer cell lines. Data obtained from caBIG

2010-12-31 | GSE21347 | GEO

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: gene expression

Project description:10 Breast cancer cell lines profiled on the Affymetrix U133 Plus 2.0 platform used in conjunction with matched DNA copy number and DNA methylation data for integrative analysis. In total, 10 samples were used. The MCF10A profile used as normal was obtained from GSM254525 and the remaining 2 cell lines were obtained from caBIG. Full RMA normalized expression profile is attached.

2010-11-05 | E-GEOD-17768 | biostudies-arrayexpress

Characterization of novel ovarian tumor cell lines that retain the phenotype of primary tumors

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-06-16 | E-GEOD-40788 | biostudies-arrayexpress