Evaluation of copy number alterations in the Ewing's Sarcoma cell line SKES1 with Affymetrix 500k SNP microarray
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Carlos Mackintosh
PROVIDER: E-GEOD-20356 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE20355: BAC-microarrays aCGH data from 67 Ewing's Sarcoma tumor samples and 16 Ewing's Sarcoma cell lines GSE20356: Evaluation of copy number alterations in the Ewing's Sarcoma cell line SKES1 with Affymetrix 500k SNP microarray GSE20357: Expression data from DTL silenced-Ewing Sarcoma's cell lines along with their controls Refer to individual Series
2011-07-31 | E-GEOD-20368 | biostudies-arrayexpress
Project description:As a result of a copy number alterations study (BAC-microarray), the SKES1 cell line was found to harbour a microdeletion in 16q23.2 SNP microarrays were applied in order to accurately delimit this alteration, finding a microdeletion of 1.04 Megabases in size.
2011-08-01 | GSE20356 | 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:Genomic changes in low and highly metastatic A549 cells were analyzed by 500K SNP arrays. A large number of genomic alterations were present in A549 cells but no significant differences were observed between the low or highly metastatic A549 cell lines. We generated a NSCLC line with highly increased propensity to form tumor nodules in murine lungs after intravenous injections. Extravasation and growth at a distant site are important parts of the metastatic process and we regarded these as a surrogate marker for in vivo aggressiveness and potential metastatic capability. A549 lung asdenocarcimona cell line with initially low metastatic potential was used for this purpose; these cells formed multiple small nodules in NOD/SCID mice after first i.v.-injection, round 1 (R1). Removal of tumor nodules from the lungs and subsequent re-injection led to a rapid increase in metastatic capacity. A highly aggressive phenotype which was stable over time was evident after three rounds (R3) of in vivo selection for the A549 cell line.
2013-02-21 | E-GEOD-44549 | biostudies-arrayexpress
Project description:The current multistep carcinogenesis models of colon cancer do not fully capture the genetic heterogeneity of the disease, which is additionally complicated by the presence of passenger and driver genetic alterations. The aim of the present study was to select in the context of this significant heterogeneity additional genes functionally related to colon cancer development. Methods: High-throughput copy number and gene expression data of 36 microsatellite stable sporadic colon cancers resected from patients of a single Institution characterized for mutations in APC, KRAS, TP53 and loss of 18q were analyzed. Genes whose expression correlated with the underlying copy number pattern were selected and their association with the above listed mutations and overall survival was evaluated. Results: Gain of 20q was strongly associated with TP53 mutation, and overall survival with alterations on 7p, 8p, 13q, 18q and 20q. An association with 18q loss and gain of 8q24 was also observed. New candidate genes with a potential role in colon cancer are PLCG1 on 20q, DBC1 on 8q21 and NDGR1 on 8p24. In addition an unexpected pattern of loss and mutability was found in the region upstream of KRAS gene. Conclusions: By integrating copy number alterations with gene expression and mutations in colon cancer associated genes we have developed a strategy that identifies previously known molecular features and additional players in the molecular landscape of colon cancer. A total of 48 sporadic colon cancer samples were analyzed by Affymetrix Mapping 250K Nsp SNP Arrays and 36 of them were also analyzed by Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]. Short summary: Expression data was correlated to copy number data to identify genes whose expression was induced by copy number changes. Gene dosage candidates were then evaluated for their association with gene mutation status of APC, KRAS and TP53, loss of heterozigosity of 18q and overall survival. Long summary: Raw intensity .CEL files of the SNP arrays were processed with Chromosome Copy Number Analysis Tool (v.1.5.6 Affymetrix, Santa Clara, CA) to identify chromosomal gains and losses. Forty eight normal samples from the HapMap project supplied by Affymetrix were used as an un-paired reference set [http://www.affymetrix.com/support/technical/sample_data/500k_data.affx]. All genomic coordinates of the SNP array probes were mapped to the Human Mar. 2006 assembly the UCSC genome browser. Raw intensity .CEL files of the exon arrays were processed with the Robust Multi-Array implementation of Affymetrix Power Tools (v.1.8.6) using the core set of features (22011 probesets). All plots and analysis steps following this processing were done using the R programming language version 2.9.0Bioconductor packages. The identification of statistically significant segments of aberration in the copy number data was performed using the default parameters of the KC-SMART algorithm and 1000 permutations (KCsmart v.2.2.0). The identification and annotation of genes within each aberrant segment was performed using biomaRt v.2.0.0. The list of genes was further annotated by using the cancerGenes resource, Cancer Gene Census and the list of breast and colon CAN genes listed in Wood et al. The genomic landscapes of human breast and colorectal cancers. Science 2007;318:1108-1113. Gene dosage effects across 36 samples for which gene expression and copy number data was available was assessed by evaluating the Spearman correlation of the raw continuous copy number (log-ratios) expression (log-intensity) for each genomic region surrounding each gene falling within the segments identified by KC-SMART. Prior to performing this task, to reduce the total number of correlation tests to perform, we filtered the gene expression dataset by removing all entries having no Gene Symbol annotation 17291 probesets and half the remaining dataset exhibiting the lowest variance resulting in 8645 probesets. Category package version 2.10.0 was used to apply a linear model-based test to detect enrichment of systematic high correlation in specific chromosomal bands taking into consideration the hierarchical structure of the bands. Gene expression class comparisons and survival analysis of the selected gene dosage candidates were performed using two sample t-tests and Cox proportional hazards regression. P-value adjustment of the correlation tests and the gene expression associations was performed using the step-up false discovery rate (FDR) controlling procedure of Benjamini and Hochberg. Raw data, supplementary methods and figures supplied as reproducible documentation (Sweave file) available from http://pierotti.group.ifom-ieo-campus.it/suppl/crc.html.
2010-04-10 | E-GEOD-16125 | biostudies-arrayexpress
Project description:Lynch syndrome, caused by germline heterozygous mutations of the DNA mismatch repair genes MLH1, MSH2, MSH6 and PMS2, or deletions affecting the EPCAM gene upstream of MSH2, is characterized by a predisposition to early-onset colorectal and additional extracolonic cancers. An alternative but rare cause of Lynch syndrome is a constitutional epimutation of MLH1, which is characterized by promoter methylation and transcriptional silencing of a single allele in normal tissues. Worldwide, five families with autosomal dominant transmission of a constitutional MLH1 epimutation linked to an MLH1 haplotype with two single nucleotide variants (c.-27C>A and c.85G>T) have been identified. Array-based genotyping using Affymetrix SNP 6.0 data in four of these families revealed a shared haplotype extending across a ≤2.6 Mb region of chromosome 3p22 encompassing MLH1 and additional flanking genes, indicating common ancestry. Genomic DNA from 5 carriers of the c.-27C>A and c.85G>T variants was hybridized on Affymetrix SNP6.0 array according to manufacturer's procedures
2013-04-01 | E-GEOD-45149 | biostudies-arrayexpress
Project description:Introduction: A major challenge in the interpretation of genomic profiling data generated from breast cancer samples is the identification of driver genes as distinct from bystander genes which do not impact tumorigenesis. One way to assess the relative importance of alterations in the transcriptome profile is to combine complementary analyses that assess changes in the copy number alterations (CNAs). This integrated analysis permits the identification of genes with altered expression that map within specific chromosomal regions that demonstrate copy number alterations, providing a mechanistic approach to identify the 'driver genes’. Methods: We have performed whole genome analysis of CNAs using the Affymetrix 250K Mapping array on 22 infiltrating ductal carcinoma samples (IDCs). Analysis of transcript expression alterations was performed using the Affymetrix U133 Plus2.0 array on 16 IDC samples. Twelve IDC samples were analyzed using both platforms and the data integrated. We also incorporated data from LOH analysis to identify genes showing loss of expression in LOH regions. Results: Copy number analysis results demarcated smaller boundaries for many previously reported CNAs, and in some cases, the CNAs were defined as more than a single contiguous event. Additionally, we were able to assign driver genes to these commonly reported regions using a rigorous methodology. For example, RAB25 showed a large increased expression in the tumors and mapped to the commonly reported amplification at 1q22. We also identified 5 genes in the 8q24 amplicon and TSEN4 in the 17q25 amplified region. LOH analysis confirmed some previously reported regions, and integration with copy number data determined that the detected LOH were copy neutral events. Finally, we have identified several RXR pathways that demonstrated down-regulation in IDC whose members may represent further targets of therapeutic intervention. Conclusion: We have demonstrated the utility of the application of integrated analysis using high-resolution CGH and whole genome transcript analysis for detecting driver genes in IDC. The high resolution platform allowed a refined demarcation of CNAs, and gene expression profiling provided a mechanism to detect genes directly impacted by the CNA. This is the first report of LOH in IDC using a high resolution platform. 22 IDC samples were analyzed for CNA and an overlapping 16 samples were analyzed for gene expression
2010-07-17 | E-GEOD-22839 | biostudies-arrayexpress
Project description:The role of microRNAs (miRNAs) in multiple myeloma (MM) has yet to be fully elucidated. To identify miRNAs that are potentially deregulated in MM, we investigated those mapping within transcription units, based on evidence that intronic miRNAs are frequently coexpressed with their host genes. To this end, we monitored host transcript expression values in a panel of 20 human MM cell lines (HMCLs) profiled on Affymetrix U133A oligonucleotide microarrays and focused on transcripts whose expression varied significantly across the dataset. We identified transcripts specific to six miRNA host genes (CCPG1, GULP1, EVL, TACSTD1, MEST, and TNIK) whose average changes in expression varied at least 2-fold from the mean of the examined dataset. We evaluated the expression levels of the corresponding intronic miRNAs by quantitative real-time RT-PCR. There was a significant correlation between the expression levels of MEST, EVL, and GULP1 and those of the corresponding miRNAs miR-335, miR-342-3p, and miR-561, respectively. Genome-wide profiling of the 20 HMCLs with the Affymetrix GeneChip human mapping 250K array set indicated that the increased expression of the three host genes and their corresponding intronic miRNAs was not correlated with local copy number variations. Notably, miRNAs and their host genes were overexpressed in a fraction of primary tumors with respect to normal plasma cells; however, this finding was not correlated with known molecular myeloma groups. The predicted putative miRNA targets, as well as the transcriptional profiles associated with the primary tumors, suggest that MEST/miR-335 and EVL/miR-342-3p may play a role in plasma cell homing and/or interactions with the bone marrow microenvironment. Our data support the idea that intronic miRNAs and their host genes are regulated dependently, and may contribute to the understanding of their biological roles in cancer. To our knowledge, this is the first evidence of deregulated miRNA expression in MM, providing insights that may lead to the identification of new biomarkers and altered molecular pathways of the disease. Keywords: integrative genomic analysis of miR-335, miR-342, and miR-561 in multiple myeloma This series of microarray experiments contains the genome-wide profiles of 20 HMCLs. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 90 micrograms of fragmented biotin-labelled DNA were hybridized on GeneChip® Human Mapping 250K NspI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip® Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Raw data were extracted using the Hidden Markov Model Genomic Smoothing window was set to 0. After the preprocessing, piecewise constant estimates of the underlying local DNA CN variation was calculated using the DNA copy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS).
2008-11-10 | E-GEOD-11522 | biostudies-arrayexpress
Project description:Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array. Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1). Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time. One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array. The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows. For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set. For Chromosome X, the average of the 20 normal female samples was used. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).
2010-12-16 | E-GEOD-26075 | biostudies-arrayexpress
Project description:The neural stem cell marker CD133 is reported to identify cells within glioblastoma (GBM) that can initiate neurosphere growth and tumor formation, however, instances of CD133- cells exhibiting similar properties have also been reported. Here, we show that some PTEN-deficient GBM tumors produce a series of CD133+ and CD133- self-renewing tumor-initiating cell types and provide evidence that these cell types constitute a lineage hierarchy. Our results show that the capacities for self-renewal and tumor initiation in GBM need not be restricted to a uniform population of stem-like cells, but can be shared by a lineage of self-renewing cell types expressing a range of markers of forebrain lineage. Keywords: Expression and copy number analysis of glioblastomas and neurosphere forming derivative cell lines of same. DNA analysis and Expression profiling: DNA from patient tumor mincates was profiled for copy number changes on Affymetrix 500k chips and sequenced for mutations in exons 4-8 of p53 and exons 5&6 of PTEN. For determination of amplification, samples with mean relative copy number estimates of >3 for SNPs residing within the locus were scored as amplified. Copy number losses were determined using data from 30 SNPs within or immediately flanking the locus of interest. Relative copy number losses that were statistically significant at the p<.001 level were scored as losses regardless of the magnitude of the alteration. DNA from neurosphere lines was analyzed for copy number alterations by profiling on Agilent 244K arrays. Relative copy number estimates were determined using the GLAD segmentation algorithm. For expression profiling, RNA was extracted as previously described (Phillips et al., 2006) and profiled on Agilent WHG (for patient samples) or WHG 4x44 chips (for neurosphere lines and grafts) according to the manufacturer's (Agilent technologies, Palo Alto CA) protocol.
2010-04-21 | E-GEOD-19612 | biostudies-arrayexpress