Affymetrix SNP copy number data for embryonic stem cell samples
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: William Freed
PROVIDER: E-GEOD-64241 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Lenalidome is a drug especially effective in low risk myelodysplastic syndromes (MDS) with isolated 5q deletion. However, 25% of the patients did not respond. TP53 mutations have been described to play a role in the disease progression, and karyotypic complexity also has an important impact in the outcome. We selected 53 MDS patients with 5q deletion and treated with lenalidomide and we studied by the following techniques: conventional G-banding cytogenetics (CC), single nucleotide polymorphism arrays (SNP-A) and sequencing, in order to assess their impact on treatment response and disease progression. Low karyotypic complexity (by CC), a high baseline platelet count (>280x103/L) and TP53 unmutated gene status are associated with the achievement of hematological response (P=0.005, P=0.008 and P=0.057, respectively). In a multivariate model, the most important predictors for lenalidomide failure are karyotypic complexity (P=0.014) and a platelet count below 280x103/L (P=0.042). Additionally, none of the TP53 mutated cases achieved complete cytogenetics response. Nevertheless, inclusion of defects by SNP-A did not allow for a better separation of responders and non responders. These findings constitute a useful reference data to be considered before lenalidomide treatment enrollment. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from bone marrow or peripheral blood and, in some cases, also lymphocytes CD3 isolated from peripheral blood samples. Copy number analyses of Affymetrix 250K and 6.0 SNP arrays were performed for 53 MDS with 5q deletion samples. There are also 30 samples from lymphocytes CD3 isolated from peripheral blood, which were used as germ-line DNA (control).
2013-07-01 | E-GEOD-35656 | biostudies-arrayexpress
Project description:Gene modified autologous hematopoietic stem cells (HSC) can provide significant clinical benefits to patients suffering from X-linked chronic granulomatous disease (X-CGD), a rare inherited immunodeficiency characterized by recurrent, often life threatening bacterial and fungal infections. Here we report on the molecular and cellular events observed in two patients treated by gene therapy in 2004. After the initial resolution of bacterial and fungal infections, both patients exhibited silencing of transgene expression due to methylation of the viral promoter, and myelodysplasia with monosomy 7 as a result of insertional activation of EVI1. One patient died from overwhelming sepsis 27 months after gene therapy, whereas a second patient underwent an allogeneic HSC transplantation. Our data shows that forced overexpression of MDS1/EVI1 or EVI1 in human cells disrupts normal centrosome duplication, linking MDS1/EVI1 activation to the development of genomic instability, monosomy 7 and clonal progression towards myelodysplasia. Genomic copy number alterations were detected by analyzing the fluorescence signal intensities of each SNP on the GeneChip Human Mapping 100K array st (Affymetrix, Santa Clara, Ca) with the Copy Number Analyzer for Affymetrix GeneChip 100K arrays (CNAT) version 2.0. The log2 ratio of each SNP, the local averaged log2 signal ratio (averaged for 10 SNPs) and the inferred chromosome copy number according to the Hidden Markov Model (HMM) were calculated. Copy number analysis of Affymetrix 100K SNP arrays was performed for one young adult with the X-linked chronic granulomatous disease (X-CGD)
2010-01-12 | E-GEOD-19523 | biostudies-arrayexpress
Project description:Circulating tumor cells (CTCs) are critical in the development of distant organ tumor metastasis, and are associated with advanced cancer stage and poor patient outcome. Here, we present the first genome-wide nucleotide-level characterization of CTCs. Our single-nucleotide polymorphism (SNP) analysis in patients with melanoma involved: 1) global comparative genomic analysis of CTCs and matched regional metastases, 2) identification of key genomic aberrations in CTCs, 3) verification of these target genes in aggressive distant tumor metastases, and 4) evidence of selective expression and functional consequence of CTC-associated genes in melanomas. We report 131 aberrant loci in CTCs that are potentially pro-metastatic, and show that such expression of a 5-marker gene panel (CSMD2, CNTNAP5, FLJ14051, ADAM6, TRPM2) in melanomas confers prognostic utility. Successful treatment of melanoma requires understanding of the metastatic process and identification of patients with tumors most likely to develop aggressive metastatic disease. Melanomas are heterogeneous, and CTCs have long been recognized as vehicles for cancer spread, representing particularly aggressive tumor clones that can evolve into successful clinical metastases. Elucidation of genomic aberrations in CTCs will aid in the development of prognostic biomarkers and therapeutic strategies to target CTCs to prevent or control distant cancer spread. This study provides the first detailed genomic confirmation of the close relation between CTCs and tumor metastases, and illustrates how CTCs can be utilized as a novel approach and rational source for identification of pro-metastatic genes in cancer research. Three individual patient cohorts were utilized in the study. CNV and LOH loci were evaluated initially in metastatic melanoma patients (n=13) in a discovery cohort. SNP loci that harbored CNV/LOH in CTCs were then separately verified for: (a) presence in distant organ metastasis (AJCC Stage IV melanoma) (n=27), and (b) relevance to prognosis in regional melanoma metastasis (AJCC Stage III melanoma) (n=35). The first discovery patient cohort group was utilized for capture of CTCs, and consisted of peripheral blood mononuclear cell (PBMC) and tumor specimens from metastatic melanoma patients (n=13). CTC-related loci were verified in a second cohort of patients with Stage IV distant organ metastases (n=27), including 15 brain, 4 lung, and 8 gastrointestinal (bowel, liver) metastases. The third patient cohort consisted of early passage (<12) established melanoma cell lines derived from 35 regional melanoma metastases (Stage III) for evaluation of the prognostic utility of the CTC-associated aberrant loci.
2014-07-01 | E-GEOD-43934 | biostudies-arrayexpress
Project description:Using xenograft-based experimental evolution, we characterize the full life history from initiation to metastasis of a tumor at the genomic and transcriptomic levels. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell lines or xenograft tumor samples.
2014-11-27 | E-GEOD-63630 | biostudies-arrayexpress
Project description:Human pluripotent stem cells commonly undergo adaptive changes during prolonged passaging in vitro. We have developed a new laminin-521 based method for self-renewal of human pluripotent stem cells. SNP6.0 array was used to assess genetic stability of several human ES cell lines cultured in the new system with two lines (H1 and HS401) cultured on feeders (standard conditions) Two main objectives in this study: To compare the number of the CNVs in human ES cells at early and late passages; for example, samples HS980 p6 and HS980 p31 represent HS980 cells at passages 6 and 31, respectively. The overall conclusion is that the observed number of CNVs is similar in the cells at early and late passages. This analysis can be remade without the reference samples. To compare the number of CNVs in control human ES cells (H1 and HS401) grown under standard protocol with that in cells (HS980, HS983a, HS999, HS916, and HS1001) grown under a new, developed by us, protocol. Because the cells were from different individuals, we could not compare them directly. Instead, we compared them to a set of samples from 75 healthy individuals, and then with each other. For the Reference These samples had been hybridized in the same lab as our samples, but for a different project; and the data were kindly provided by Prof. Kere. However, the same overall conclusion would result from an other sufficiently large dataset of healthy human individuals. Please note that 75 healthy individual samples had been hybridized in the same lab as our samples and the data were kindly provided by Prof. Kere, which is linked as a Series supplementary file ('75_samples_ref.REF'). It is a Reference Model File that Affymetrix Genotyping Console software has created based on data from 75 healthy individuals (i.e. processed file based on the CEL files of the 75 healthy individuals). The file derives from the "CN/LOH Reference Model File Creation and Analysis (Batch Sample Mode)" process according to the Genotyping Console manual. It contains SNP-wise information on the observed distribution of hybridization intensities of a set of samples that are assumed to be diploid in copy number (for most part of their genomes at least). This file is then used to compare the intensities observed in the CEL files of interest to infer deviations from the reference as CNVs. Thus, in combination with the CEL files (from each ES cell line), this file enables the exact replication of the CNV analyses done for the various human ES cell lines study. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted cultured human ES cells. Several lines were analysed at different time points of the experiment. The analysis was done using default parameters and comparing each sample against a reference set of 75 healthy individuals provided by Juha Kere.
2013-12-19 | E-GEOD-53436 | biostudies-arrayexpress
Project description:In this study, copy number variations of hiPSCs were compared to their parental fibroblast lines and hESCs to assess the level of DNA damage incurred due to the process of reprogramming of somatic cells. Higher levels of copy number changes were observed in hiPSCs (especially in early passage hiPSCs) compared to the other cell types. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from in vitro cultured cells. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 35 hiPSC samples, 2 hESC samples, and 5 fibroblast samples. Other hESC and the reference Hapmap sample CEL files were obtained from Narva et al. 2010, Nat. Biotech., GEO accession code GSE15097 (see readme file below for details).
2011-01-31 | E-GEOD-26173 | biostudies-arrayexpress
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:Somatic DNA alteration underlies tumor development and progression, and gives rise to tumors with diverse genetic contexts. Here, we identify in a collection of 29 colorectal cancer cell lines and 226 primary colorectal tumors recurrent amplification of chromosome 13, an alteration highly restricted to colorectal-derived cancers. A minimal region of amplification on 13q12.2 pinpoints caudal type homeobox transcription factor CDX2, a master regulator of anterior-posterior patterning, midgut development, and intestinal epithelial cell differentiation and maintenance. In contrast to its described role as a colorectal tumor suppressor, we show that in the context of genomic amplification, CDX2 is required for proliferation and anchorage-independent growth of colorectal cancer cells. By genome-wide expression and location analysis, we reveal that CDX2 directly promotes expression of Wnt pathway genes. Further results suggest that CDX2 induces expression of intestinal differentiation markers and modulates b-catenin transcriptional activity. These data characterize CDX2 as a novel lineage-survival oncogene deregulated in colorectal cancer. Genome-wide DNA copy number analysis of cell line COLO320 by Affymetrix SNP 6.0 array
2012-11-02 | E-GEOD-30182 | biostudies-arrayexpress
Project description:Comparison between the copy number of differentially methylated sites between lymph node metastasis from melanoma patients with good prognosis and melanoma brain metastasis. All samples are taken from different patients, and were established as cell lines in the John Wayne Cancer Institute. Sixteen metastatic melanomas were run on Affymetrix Genome-Wide Human SNP Array 6.0. Lymph node metastases and brain metastases genetic copy number variations were compared.
2013-09-19 | E-GEOD-44019 | biostudies-arrayexpress
Project description:Affymetrix SNP array analysis was performed on DNA extracted from whole blood samples of 7 Taiwanese patients with hyperlipidemia. Three copy number variant (CNV) regions associated significantly with hyperlipidemia were identified through genomic segmentation analysis (P<0.001). 7 male Taiwanese hyperlipidemia patients.
2015-05-01 | E-GEOD-38149 | biostudies-arrayexpress