SNP array analysis on Maffucci tumours
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Twinkal Pansuriya
PROVIDER: E-GEOD-26674 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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
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
Project description:This SuperSeries is composed of the following subset Series: GSE22855: Comparison of enchondromas with controls (growth plate and cartilage) GSE22984: Affymetrix SNP6.0 on Ollier disease-related tumors Refer to individual Series
2011-08-25 | E-GEOD-22965 | biostudies-arrayexpress
Project description:Development of a new carcinoma cell line (HC-AFW1) derived from a pediatric liver tumor The cell line HC-AFW1 was derived from a 4 year old boy suffering from HCC through culturing and passage into immuno-deficient mice. The cell line is stable now for over 8 months of culture with a doubling time of 40 h. The tumor cells show an epithelial histology and express hepatoma proteins such as Alpha-fetoprotein (AFP), Glypican 3, E-cadherin, CD10, CD326, HepPar1, Vimentin and Desmin. Catenin beta shows a deletion of 49 amino acids in the exon 3 involving the phosphorylation sites of GSK3 and is detectable in the cell nuclei. Cytogenetic analysis revealed large anomalies in the chromosomal map including chromosomal aberrations found in hepatoblastoma as well as in adult HCC. Copy number analysis of two different passages of HC-AFW1 cells Two tumor specimens were used for tissue culture and xenotransplantation into NSG mice. Tumor cells derived from xenografts were cultured and designated as HC-AFW1. DNA was analyzed from the passage 2 (2P2). HC-AFW2 was derived from tissue culture without transfer in to mice. Primary tissue samples were minced into pieces of 3x3 mm and cultured on 6 well plates (Becton Dickenson, Frankfurt, Germany) in DMEM (GIBCO BRL, Carlsbad, CA) supplemented with 10% FCS (growth medium). Cell cultures were maintained in a humidified atmosphere containing 5% CO2 at 37°C. For subculturing cells were detached from the culture surface using accutase in Dulbecco´s PBS containing 0.5mM EDTA (PAA Laboratories GmbH, Cölbe, Germany) for 2-3 minutes at 37°C. A sub-cultivation ratio of 1:4 and 1:6 was performed twice per week. Cells were stored in liquid nitrogen as a suspension in complete growth medium with 10% DMSO. DNA from patient blood and tumor samples was isolated with the QiaAmp DNA mini Kit according to manufacturer's instructions (Qiagen, Hilden, Germany). Single nucleotide polymorphism (SNP) and copy number polymorphism (CNP) genotyping were performed using the Genome-Wide Human SNP Array 6.0 and Genotyping Console (GTC) software (Affymetrix, Santa Clara, CA).
2011-12-01 | E-GEOD-29283 | biostudies-arrayexpress
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.
2011-07-19 | GSE26674 | GEO
Project description:A subset of ovarian cancer are characterized by 19q12 amplification. To perform funtional studies of this amplicon the profile has been determined by SNP analysis. Affymetrix SNP arrays were performed according to the manufacturer's directions on genomic DNA extracted from ovarian cancer cell lines OVCAR-3 and FU-OV-1
2010-12-24 | E-GEOD-26301 | biostudies-arrayexpress
Project description:Alterations of the short arm of chromosome 12 (12p) occur in various hematological malignancies and ETV6 and CDKN1B, which are located on 12p, have been implicated as leukemogenic genes of interest. Design and Methods: We selected 7 patients with myeloid malignancies and small 12p deletions by FISH encompassing only the region centromeric of ETV6 and further evaluated them by SNP microarrays. Results: The minimal deleted region (MDR) contained nine genes only. These genes were subsequently analyzed by microarray expression profiling in an independent cohort of 781 cases mostly with different hematological malignancies or without any hematological malignancy: CREBL2, MANSC1, and CDKN1B were expressed in >25% of cases, while the other 6 genes were expressed in a minority of cases only. As CDKN1B is a cell cycle regulator and functions as a tumor suppressor gene, this gene was selected for further expression studies in 286 AML patients. In cases with low CDKN1B expression (expression level <1,160; 1st quartile), RUNX1-RUNX1T1 (11/83; 13.3%; vs. 5/203; 2.5%; p=0.001), PML-RARA rearrangements (11/83; 13.3%; vs. 4/203; 2.0%; p<0.001), 11q23/MLL rearrangements (6/83; 7.2%; vs. 4/203; 2.0%; p=0.038), and FLT3-TKD mutations (7/63; 11.1% vs. 6/167; 3.6%; p=0.047) were more frequently observed than in patients with intermediate/high expression (2nd-4th quartiles). Low CDKN1B expressers had longer median OS and EFS (not reached vs. 14.9 months; p=0.005 and 31.0 vs. 9.7 months; p=0.013, respectively) than intermediate/high expressers. Conclusions: CDKN1B is an interesting candidate gene as a potential biomarker for acute myeloid leukemia prognostication. Affymetrix SNP arrays were performed according to the manufacturer's directions using DNA extracted from mononuclear cells after Ficoll density centrifugation from bone marrow or peripheral blood samples.
2011-12-16 | E-GEOD-27832 | biostudies-arrayexpress
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.
2011-07-19 | GSE26667 | GEO
Project description:Ollier disease and Maffucci syndrome are non-hereditary skeletal disorderscharacterized by multiple enchondromas (Ollier disease) combined with spindle cellhemangiomas (Maffucci syndrome). Somatic heterozygous IDH1 (R132C and R132H) orIDH2 (R172S) mutations were found in 87% of enchondromas, benign cartilage tumors,as well as in 70% of spindle cell hemangiomas, benign vascular lesions. In total, 35 of 43(81%) patients with Ollier disease and 10 of 13 (77%) patients with Maffucci syndromecarried IDH1 (98%) or rarely IDH2 (2%) mutations in their tumors. Fourteen patientswith multiple tumors at different anatomic locations displayed identical mutations inseparate lesions. Since in other tumor types the presence of an IDH1 mutation is strongly associated withhypermethylation 26, 27, we assessed whether there was a difference in methylation patternof enchondromas with (n = 8) and without (n = 4) IDH1 mutations detactable at Sangersequencing. Methylation and expressionprofiling showed that IDH1 mutations in cartilage tumors are associated withhypermethylation and downregulation of the expression of several genes. Total 12 samples which includes 8 enchondromas with IDH1 mutation (4 Ollier enchondromas, 2 Maffucci enchondromas and 2 solitary enchondromas) and 4 enchondromas (1 Ollier enchondroma, 3 solitary enchondromas) without IDH1 or IDH2 mutations were used. Of these 4 enchondromas without IDH1 mutation, one had R132G IDH1 mutated cells present in the subpopulation, below the threshold level of Sanger sequencing. Bisulfite treatment was performed using EZ DNA Methylation™ Kit (ZymoResearch, Orange, CA). Bisulphite converted DNA was then hybridized to IlluminaHumanMethylation27 BeadChip (Illumina Inc., San Diego, CA) by followingmanufacturer’s instructions. Infinium Unsupervised clustering analysis was performed 25 using the Ward’s clustering algorithm based on Euclidian distance. The 2000 most variable CpG sites (excluding those on the X and Y chromosomes) were used in the clustering analysis.
2011-11-05 | E-GEOD-31337 | biostudies-arrayexpress
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