Array-CGH analysis of X chromosome of XLMR patient
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE10049 | GEO | 2008/05/27
SECONDARY ACCESSION(S): PRJNA108621
REPOSITORIES: GEO
Similar Datasets
Project description:Mental retardation (MR) is a non-progressive cognitive impairment affecting 2 to 3% of the Western population. So far, point mutations and subtle deletions and insertions have been shown to represent only a proportion (<40%) of genetic causes underlying X-linked mental retardation (XLMR). We have screened a subset of 300 presumable X-linked families by X chromosome-specific array-CGH and identified 6 families with overlapping microduplications at Xp11.22 containing two candidate genes; both of which showed overexpression in the affected individuals. Array-CGH data revealed aberrant Cy5/Cy3 log2 ratios for different but overlapping sets of clones indicating varying sizes of these duplications in the different families. Keywords: comparative genomic hybridization
2008-02-20 | GSE9143 | GEO
Project description:Array-CGH analysis of X chromosome of XLMR patient Keywords: comparative genomic hybridization Comparison of 6 patient samples in 2 dyes; samples XY1, Xy2, and XY3 can be considered as control samples.
2008-05-27 | E-GEOD-10049 | biostudies-arrayexpress
Project description:Mental retardation (MR) is a non-progressive cognitive impairment affecting 2 to 3% of the Western population. So far, point mutations and subtle deletions and insertions have been shown to represent only a proportion (<40%) of genetic causes underlying X-linked mental retardation (XLMR). We have screened a subset of 300 presumable X-linked families by X chromosome-specific array-CGH and identified 6 families with overlapping microduplications at Xp11.22 containing two candidate genes; both of which showed overexpression in the affected individuals. Array-CGH data revealed aberrant Cy5/Cy3 log2 ratios for different but overlapping sets of clones indicating varying sizes of these duplications in the different families. X chromosome-specific array-CGH performed for probands of families A, FAM3, B, MRX17, C, MRX31, and D, A057, revealing the duplications at Xp11.22. DNA from two unrelated MR patients were differentially labeled and co-hybridized onto the X-array. The patients with duplications were hybridized in Cy5 against unrelated MR patients, named Pat XY1-6, in the Cy3 channel.
2010-06-25 | E-GEOD-9143 | biostudies-arrayexpress
Project description:Array comparative genomic hybridization (CGH) analysis of ameloblastoma tumor
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Project description:Array Comparative Genomic Hybridization (CGH) profiling of Oral Sqaumaous Cell Carcinoma (OSCC) was performed to delineate candidate non-random chromosomal loci associated with clinico-pathological parameters. The array CGH hybridizations were performed for 60 OSCC samples with pooled gender matched controls. All tissue samples were collected after obtaining written informed consent.
2011-03-11 | GSE23831 | GEO
Project description:A series of studies have been published that evaluate the chromosomal copy number changes of different tumor classes using array Comparative Genomic Hybridization (array CGH), however the chromosomal aberrations that distinguish the different tumor classes have not been fully characterized. Therefore, we performed a meta-analysis of different array CGH data sets in an attempt to classify samples tested across different platforms. As opposed to RNA expression a common reference is used in dual channel CGH arrays: normal human DNA, theoretically facilitating cross-platform analysis. To this aim, cell line and primary cancer data sets from three different dual channel array CGH platforms obtained by four different institutes were integrated. The cell line data were used to develop preprocessing methods which performed noise reduction and transformed samples into a common format. The transformed array CGH profiles allowed perfect clustering by cell line, but importantly not by platform or institute. The same preprocessing procedures used for the cell line data were applied to data from 373 primary tumors profiled by array CGH, including controls. Results indicated that there is no apparent feature related to the institute or platform and that array CGH allows for unambiguous cross-platform meta-analysis. Major clusters with common tissue origin were identified. Interestingly, tumors of hematopoietic and mesenchymal origins cluster separately from tumors of epithelial origin. Therefore it can be concluded that chromosomal aberrations of tumors from hematopoietic and mesenchymal origin versus tumors of epithelial origin are distinct, and these differences can be picked up by metaanalysis of array CGH data. This suggests the possibility of prospectively using combined analysis of diverse copy number datasets for cancer subtype classification. Keywords: comparative genomic hybridization, meta-analysis, cancer
2006-08-29 | GSE5051 | GEO
Project description:Array comparative hybridization (array-CGH) for detection of gene dose alterations in VACTERL association
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Project description:Array Comparative Genomic Hybridization (CGH) profiling of Oral Leukoplakia (OPL) and early stage Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate non-random chromosomal loci associated with disease progression and clinico-pathological parameters. The array CGH hybridizations were performed for 24 OPL and 38 OSCC samples with pooled gender matched controls. All tissue samples were collected after obtaining written informed consent.
2017-04-26 | GSE85514 | GEO
Project description:Osteosarcoma (OS) is a very aggressive bone tumor characterized by highly abnormal complex karyotypes.This a-CGH is a part of an expriment whose aim was to identify, genomic imbalance, DNA methylation and gene expression profiles of osteosarcoma cell lines. Keywords: comparative genomic hybridization
2009-05-01 | GSE11411 | GEO
Project description:We present the first computational approach to reconstruct the sequence of copy number alterations driving carcinogenesis from the analysis of several tumor samples of a same patient. Applied to BAC array-CGH and SNP array data from bladder and breast cancers, this method proved highly valuable to establish the clonal relationships between primary tumors and recurrences and to identify the chromosome aberrations at the initiation of tumorigenesis. Keywords: Comparative Genomic Hybridization
2009-12-01 | GSE19193 | GEO