GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array; Methylation profiling by array

Platforms:

GPL9183 GPL4091 GPL3720

148 Samples

Download data: CEL, TXT

(Submitter supplied) The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL9183

58 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

30 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL3720

60 Samples

Download data: CEL, XLS

(Submitter supplied) Genomic abnormalities leading to colorectal cancer (CRC) include somatic events causing copy number aberrations (CNAs) as well as copy neutral manifestations such as loss of heterozygosity (LOH) and uniparental disomy (UPD). We studied the causal effect of these events by analyzing high resolution cytogenetic microarray data of 15 tumor-normal paired samples. We detected 144 genes affected by CNAs. A subset of 91 genes are known to be CRC related yet high GISTIC scores indicate 24 genes on chromosomes 7, 8, 18 and 20 to be strongly relevant. Combining GISTIC ranking with functional analyses and degree of loss/gain we identify three genes in regions of significant loss (ATP8B1, NARS, and ATP5A1) and eight in regions of gain (CTCFL, SPO11, ZNF217, PLEKHA8, HOXA3, GPNMB, IGF2BP3 and PCAT1) as novel in their association with CRC. Pathway analysis indicates TGF-β signaling pathway to be affected by the cytogenetic events causing CRC as evidenced by the action of genes impacted by CNAs on SMAD family of proteins. Finally, LOH and UPD collectively affected nine cancer related genes. Transcription factor binding sites on regions of >35% copy number loss/gain influenced 16 CRC genes. Our analysis shows patient specific CRC manifestations at the genomic level and that these different events affect individual CRC patients differently.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array; Genome variation profiling by SNP array

Platform:

GPL16131

30 Samples

Download data: CEL, TXT

(Submitter supplied) Identification of Acquired Copy Number Alterations and Uniparental Disomies in Cytogenetically Normal Acute Myeloid Leukemia Using High-Resolution Single Nucleotide Polymorphism Analysis Recent advances in genome-wide single nucleotide polymorphism (SNP) analyses have revealed previously unrecognized microdeletions and uniparental disomy (UPD) in a broad spectrum of human cancers. As acute myeloid leukemia (AML) represents a genetically heterogeneous disease, this technology might prove helpful especially for cytogenetically normal AML (CN-AML) cases. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

4 related Platforms

510 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Structural changes of chromosomes play important roles in the carcinogenesis of colorectal carcinoma (CRC). Here, by using SNP-typing arrays, we have tried to screen for recurrent chromosome copy number changes and loss-of-heterozygosity in the genome of colorectal carcinoma. Genomic DNA was isolated from tumor and paired normal tissues of CRC (n=94), and was hybridized to Affymetrix Mapping 50K Xba 240 arrays. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL2005

188 Samples

Download data: CEL

(Submitter supplied) Although a number of genes related to melanoma development have been identified through candidate gene screening approaches, few studies have attempted to conduct such analyses on a genome-wide scale. Here we use Illumina 317K whole-genome single-nucleotide polymorphism arrays to define a comprehensive allelotype of melanoma based on loss of heterozygosity (LOH) and copy number changes in a panel of 76 melanoma cell lines. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL5711

76 Samples

Download data

(Submitter supplied) Genomic imprinting is a mechanism in which gene expression varies depending on parental origin. Imprinting occurs through differential epigenetic marks on the two parental alleles, with most imprinted loci marked by the presence of differentially methylated regions (DMRs). To identify sites of parental epigenetic bias, here we have profiled DNA methylation patterns in a cohort of 57 individuals with uniparental disomy (UPD) for 19 different chromosomes, defining imprinted DMRs as sites where the maternal and paternal methylation levels diverge significantly from the biparental mean. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

66 Samples

Download data: TXT

(Submitter supplied) A survey of the somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL8882 GPL13314

26 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL19705 GPL19706

12 Samples

Download data: TXT

(Submitter supplied) The goal of this experiment was to determine the size, genomic extent and gene content of complex rearrangements involving chromosome 9q

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19706

3 Samples

Download data: TXT

(Submitter supplied) The goal of this experiment was to determine the size, genomic extent and gene content of complex rearrangements involving multiple chromosomes

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL19705

9 Samples

Download data: TXT

(Submitter supplied) These samples include 4 patients with a triplication/ROH combination on: (1) chromosome 6, (2) chromosom 9, (3) chromosome 10, (4) chromosome 14

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL3718 GPL16131

14 Samples

Download data: CEL, CHP, CYCHP

(Submitter supplied) To obtain a comprehensive genomic profile of presenting multiple myeloma cases we performed high resolution single nucleotide polymorphism (SNP) mapping array analysis in 114 samples alongside 258 samples analysed by U133 Plus 2.0 expression array (Affymetrix). We examined DNA copy number alterations and loss of heterozygosity (LOH) in order to define the spectrum of minimally deleted regions in which relevant genes of interest can be found. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array; Expression profiling by array

Platforms:

GPL570 GPL3720 GPL3718

491 Samples

Download data: CEL, CHP

(Submitter supplied) For sporadic Burkitt lymphoma (BL) few genetic lesions are known besides the pathognomonic IG-MYC translocations. Thirtynine molecularly-defined BL were analyzed with high-resolution single-nucleotide polymorphism chips for genomic imbalances and uniparental disomy (UPD). Imbalances were correlated to transcript profiling and selected miRNA analysis. Translocations affecting the MYC locus were studied by fluoresence in situ hybridization. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL3720 GPL3718

99 Samples

Download data: CEL, CHP