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Illumina GoldenGate Methylation array data for X-CGD patients and healthy controls

ABSTRACT: 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. In line with this observation, a genome wide methylation analysis of 807 cancer related genes revealed a DNA methylation pattern characteristic of MDS and AML patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE19515 | GEO | 2009/12/17

SECONDARY ACCESSION(S): PRJNA122339

REPOSITORIES: GEO

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Illumina GoldenGate Methylation array data for X-CGD patients and healthy controls

Project description: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. In line with this observation, a genome wide methylation analysis of 807 cancer related genes revealed a DNA methylation pattern characteristic of MDS and AML patients. Genomic DNA was prepared from peripheral blood cells of patient 1 (d 0 and month 27) and 25 healthy controls including 12 males and 13 females. The GoldenGate Methylation Cancer Panel I array was used to compare methylation degree in 1.505 CpG sites from promoter regions or the first exon of 807 mostly cancer related genes between the patient 1 (d 0 and month 27) and 25 healthy controls.

2010-06-24 | E-GEOD-19515 | biostudies-arrayexpress

Affymetrix SNP array data for Genomic Instability and Myelodysplasia with Monosomy 7

2010-01-13 | GSE19523 | GEO

Affymetrix SNP array data for Genomic Instability and Myelodysplasia with Monosomy 7

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

Developmental stage-specific interplay between GATA1 and IGF signaling in fetal hematopoiesis and leukemogenesis

Project description:This SuperSeries is composed of the following subset Series: GSE16676: Rescue of murine Gata1s mutant M7 leukemic cells by full-length Gata1 GSE16677: Gene expression profiling of Down Syndrome (DS)-AMKL and non-DS AMKL samples GSE16679: Plag1 overexpression cooperates with Evi1 overexpression and Gata1s mutation in leading to M7 leukemia GSE16682: Murine M7 leukemia derived from retroviral insertional mutagenesis of Gata1s fetal progenitors GSE16684: Murine M7 leukemia derived from retroviral insertional mutagenesis of Gata1s fetal progenitors depends on IGF signaling Refer to individual Series

2010-08-01 | E-GEOD-16655 | biostudies-arrayexpress

Homo sapiens

Project description:Affymetrix SNP array data for Genomic Instability and Myelodysplasia with Monosomy 7

| PRJNA122235 | ENA

DNA Methylation Biomarkers for Noninvasive Diagnosis of Colorectal Cancer

Project description:DNA methylation in colorectal cancer diagnosis. The Illumina GoldenGate Methylation Cancer Panel I was used to select a set of candidates markers informative of colorectal cancer diagnosis from 807 cancer-related genes. In the discovery phase, tumor tissue and paired adjacent normal mucosa from 92 colorectal patients were analyzed.

2013-05-27 | GSE43369 | GEO

Goldengate Methylation analysis: Ewing Sarcoma

Project description:Methylation array analysis of Ewing sarcoma primary tumors and cell lines compared to mesechymal stem cells

2012-09-01 | GSE36857 | GEO

Methylation analysis of cancer and control samples.

Project description:DNA methylation profiling of cancer and control samples. The Illumina GoldenGate Methylation Cancer Panel I was used to obtain DNA methylation profiles across 1,505 CpG sites CpGs distributed across 807 genes in blood DNA specimens.

2012-11-01 | GSE33614 | GEO

Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features

Project description:The Illumina GoldenGate® methylation array was used to evaluate DNA methylation at 1,505 CpG sites in 807 cancer-related genes in 91 consecutive CRC samples and 28 matched normal colonic mucosa.

2012-07-18 | GSE39446 | GEO

Diagnostic and prognostic utility of a unique epigenetic prognostic PHYMA signature in prostate cancer

Project description:Genome wide DNA methylation profiling of normal and Prostate cancer samples. The Illumina GoldenGate Methylation Cancer Panel I with 1,505 CpG sites selected from 807 genes was used to obtain DNA methylation profiles. Samples included 24 normals and 87 tumors.

2014-03-13 | GSE39603 | GEO

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