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Detection of copy number variation in patients with Pelizaeus-Merzbacher disease (PMD) - NimbleGen

ABSTRACT: The objective of the study was to investigate the extent of duplicated, triplicated, and quadruplicated regions in PMD patients so that junction analysis could be performed. 10 samples were analyzed. Replicates are not included. The arrays were performed as a service by NimbleGen. Reference DNA was normal male NM002 from our lab.

ORGANISM(S): Homo sapiens

SUBMITTER: Grace Hobson

PROVIDER: E-GEOD-63949 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Detection of copy number variation in patients with Pelizaeus-Merzbacher disease (PMD)

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

2015-02-09 | E-GEOD-64122 | biostudies-arrayexpress

Detection of copy number variation in patients with Pelizaeus-Merzbacher disease (PMD) - NimbleGen

Project description:The objective of the study was to investigate the extent of duplicated, triplicated, and quadruplicated regions in PMD patients so that junction analysis could be performed.

2015-02-09 | GSE63949 | GEO

Detection of copy number variation in patients with Pelizaeus-Merzbacher disease (PMD) - Affymetrix

Project description:The objective of the study was to investigate the extent of duplicated, triplicated, and quadruplicated regions in PMD patients so that junction analysis could be performed.

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Detection of copy number variation in patients with Pelizaeus-Merzbacher disease (PMD) - Affymetrix

Project description:The objective of the study was to investigate the extent of duplicated, triplicated, and quadruplicated regions in PMD patients so that junction analysis could be performed. 4 samples were analyzed. Replicates are not included.

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Profiling DNA copy number alterations of myxofibrosarcomas with NimbleGen array CGH chips

Project description:Characterized by a wide histological spectrum, myxofibrosarcoma ranges from deceptively bland-appearing lesions to frankly pleomorphic sarcomas, representing a suitable model to elucidate the molecular aberrations in multistep disease progression. To explore cancer-associated genes of myxofibrosarcoma, ultrahigh-resolution array comparative genomic hybridization (aCGH) was used to profile DNA copy number alterations in myxofibrosarcoma tumor samples and cell lines. Along with normal reference DNA, 12 tumor samples and 2 cell lines (NMFH-1, OH931) of human myxofibrosarcoma were extracted for genomic DNAs, which were subjected to manufacturer’s (NimbleGen Inc) outsourcing service of DNA labeling, hybridization, and normalization of data obtained from 385K oligonucleotide array CGH chips.

2012-02-02 | E-GEOD-35483 | biostudies-arrayexpress

MCL1 is deregulated in subgroups of diffuse large B-cell lymphoma

Project description:MCL1 is an anti-apoptotic member of the BCL2 family that is deregulated in various solid and hematological malignancies. However, its role in the molecular pathogenesis of diffuse large B-cell lymphoma (DLBCL) is unclear. We analyzed gene expression profiling data from 350 DLBCL patient samples and detected that activated B-cell-like (ABC) DLBCLs express MCL1 at significantly higher levels compared to germinal center B-cell-like (GCB) DLBCL patient samples (p=2.7 x 10(-10)) [PMID 23257783]. Immunohistochemistry confirmed high MCL1 protein expression predominantly in ABC DLBCL in an independent patient cohort (n=249; p=0.001). To elucidate molecular mechanisms leading to aberrant MCL1 expression, we analyzed array comparative genomic hybridization (aCGH) data of 203 DLBCL samples [GSE11318] and identified recurrent chromosomal gains/amplifications of the MCL1 locus that occurred in 26% of ABC DLBCLs. In addition, aberrant STAT3 signaling contributed to high MCL1 expression in this subtype. Knockdown of MCL1 as well as treatment with the BH3-mimetic obatoclax induced apoptotic cell death in MCL1 positive DLBCL cell lines. In summary, MCL1 is deregulated in a significant fraction of ABC DLBCLs and contributes to therapy resistance. These data suggest that specific inhibition of MCL1 might be utilized therapeutically in a subset of DLBCLs. This GEO dataset is comprised of aCGH measurements for DLBCL cell lines, which are used in the above-mentioned paper. Cell lines were measured against the DNA of a healthy male donor who in turn was measured against a pool of healthy DNAs to correct for individual CNVs of the donor.

2013-01-04 | E-GEOD-43272 | biostudies-arrayexpress

Hybridization thermodynamics of NimbleGen microarrays.

Project description:BackgroundWhile microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets.ResultsWe demonstrate the benefits of an improved model for microarray hybridization and assess the relative contributions of the probe-target binding strength and the different competing structures. Remarkably, specific and unspecific hybridization were apparently driven by different energetic contributions: For unspecific hybridization, the melting temperature Tm was the best predictor of signal variation. For specific hybridization, however, the effective interaction energy that fully considered competing structures was twice as powerful a predictor of probe signal variation. We show that this was largely due to the effects of secondary structures in the probe and target molecules. The predictive power of the strength of these intramolecular structures was already comparable to that of the melting temperature or the free energy of the probe-target duplex.ConclusionsThis analysis illustrates the importance of considering both the effects of probe-target binding strength and the different competing structures. For specific hybridization, the secondary structures of probe and target molecules turn out to be at least as important as the probe-target binding strength for an understanding of the observed microarray signal intensities. Besides their relevance for the design of new arrays, our results demonstrate the value of improving thermodynamic models for the read-out and interpretation of microarray signals.

| S-EPMC2823707 | biostudies-literature

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The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd1 [NimbleGen]

Project description:We use a metabolic labeling strategy for directly measuring nucleosome turnover to determine the role of chromatin remodeler Chd1 on chromatin dynamics in mouse embryonic fibroblasts expressing with wildtype-Chd1 and dominant negative K510R-Chd1. We find that expression of K510R-Chd1 decreases nucleosome turnover at the promoter and increases turnover within the gene body. 10 Illumina sequencing samples and 4 Nimblegen array samples

2014-04-15 | E-GEOD-52347 | biostudies-arrayexpress

Progesterone Antagonist Therapy in a Pelizaeus-Merzbacher Mouse Mode

Project description:Pelizaeus-Merzbacher disease (PMD) is a severe hypomyelinating disease, characterized by ataxia, intellectual disability, epilepsy and premature death. In the majority of cases, PMD is caused by duplication of PLP1 that is expressed in myelinating oligodendrocytes. Despite detailed knowledge of PLP1, there is presently no curative therapy for PMD. We used a Plp1 transgenic PMD mouse model to test the therapeutic effect of Lonaprisan, an antagonist of the nuclear progesterone receptor, in lowering Plp1 mRNA overexpression. We applied placebo-controlled Lonaprisan therapy to PMD mice for 10 weeks and performed the grid slip analysis to assess the clinical phenotype. Additionally, mRNA expression and protein accumulation as well as histological analysis of the central nervous system were performed. While Plp1 mRNA levels are increased about 1.8-fold in PMD mice compared to wildtype controls, daily Lonaprisan treatment reduced overexpression at the RNA level up to 1.5-fold, which was sufficient to significantly improve a poor motor phenotype. Electron microscopy confirmed a 25% increase in the number of myelinated axons in the corticospinal tract when compared to untreated PMD mice. Microarray analysis revealed the upregulation of pro-apoptotic genes in PMD mice that could be partially rescued by Lonaprisan treatment, which also reduced microgliosis, astrogliosis, and lymphocyte infiltration.

2014-02-26 | GSE55315 | GEO

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