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Expression array using Maffucci tumours

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE26667 | GEO | 2011/07/19

SECONDARY ACCESSION(S): PRJNA142191

REPOSITORIES: GEO

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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

SNP array analysis on Maffucci tumours

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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.

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Examination of Ollier Disease and Maffucci Syndrome using IDH Tiling Array

Project description:Ollier disease and Maffucci syndrome are non-hereditary skeletal disorders characterized by multiple enchondromas (Ollier) combined with spindle cell hemangiomas (Maffucci). We found somatic heterozygous IDH1 mutations (R132C and R132H) in 83% of enchondromas, benign cartilage tumors, as well as in 40% of spindle cell hemangiomas, benign vascular lesions. In total, 33 of 42 (78%) patients with Ollier disease and 7 of 13 (54%) patients with Maffucci syndrome carried a mutation in at least one of their tumors. Twelve patients with multiple tumors at different locations displayed identical mutations in separate lesions. Immunohistochemical staining for the R132H IDH1 mutant protein suggested intraneoplastic as well as somatic mosaicism. IDH1 mutations were less frequent (63%) in high grade malignant cartilage tumors in Ollier disease, suggesting that IDH1 is less important for malignant transformation. IDH1 and IDH2 mutations were found in 36% of sporadic cartilage tumors and in four cell lines derived from sporadic chondrosarcomas.

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2011-11-05 | E-GEOD-30354 | 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

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2011-11-05 | E-GEOD-30835 | biostudies-arrayexpress

Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell haemangioma in Ollier disease and Maffucci syndrome

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