GEO DataSets

(Submitter supplied) Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, as well as genomic profiling of primary retinoblastoma samples. more...

Organism:

Homo sapiens

Type:

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

7 related Platforms

312 Samples

Download data: CEL, CSV, IDAT, XLS, XLSX

(Submitter supplied) Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic profiling of primary retinoblastoma samples. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL8887 GPL16131 GPL6985

94 Samples

Download data: CEL, CSV, IDAT, RDATA

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6985 GPL19718 GPL8693

10 Samples

Download data: TXT

(Submitter supplied) Chromothripsis represents an extreme class of complex chromosome rearrangements (CCRs) with major effects on chromosomal architecture. Although recent studies have associated chromothripsis with congenital abnormalities, the incidence and pathogenic effects of this phenomenon require further investigation. Here, we analyzed the genomes of three families in which chromothripsis rearrangements were transmitted from a female carrier to her child. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6985

2 Samples

Download data: TXT

(Submitter supplied) We carried out the analyses of chromosome variations between low-grade and high-grade gliomas in Chinese population. We found out the differences in chromosomes, cytobands, genes, pathways and GO functions.

Organism:

Homo sapiens

Type:

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

Platform:

GPL6985

36 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

Platforms:

GPL6985 GPL6244 GPL6986

22 Samples

Download data: CEL

(Submitter supplied) Inflammatory leiomyosarcoma (ILMS) is a soft tissue tumor that morphologically resembles conventional leiomyosarcoma (LMS) admixed with a prominent inflammatory infiltrate. Genetic data on ILMS are still limited but have suggested that this entity is characterized by hyperhaploidy (24-34 chromosomes). This low chromosome number is otherwise uncommon in neoplasia and has been found only in 0.2-0.3% of cytogenetically investigated tumors. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL6985 GPL6986

3 Samples

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(Submitter supplied) in 25% - 30% of all OS cases the chromosome region 17p11.2-p12 is aberrant. Using SNP array in conjunction with expression microarrays we try to identify genes which can be classified as oncogens or are in someway benificial to the survival of the tumor.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6947 GPL6985

68 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6985 GPL11157

8 Samples

Download data: CEL, CYCHP

(Submitter supplied) Acute lymphoblastic leukemia (ALL), the most common malignant disorder in childhood, is typically associated with numerical chromosomal aberrations, fusion genes or small focal deletions, thought to represent important pathogenetic events in the development of the leukemia. Mutations, such as single nucleotide changes, have also been reported in childhood ALL, but these have only been studied by sequencing a small number of candidate genes. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6985

4 Samples

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(Submitter supplied) Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyzed the genomes of ten patients with congenital disease that were preselected to carry complex chromosomal rearrangements (CCRs) with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL8855 GPL6985 GPL6979

13 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL6985 GPL8887 GPL6986

31 Samples

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(Submitter supplied) We present a computational tool, FounderTracker, for discovering founder mutations in cancer, based on the detection of significantly conserved haplotypes in tumor SNP profiles. We demonstrate the relevance of the approach by identifying founder mutations in two different cancers, and we show with simulated data that FounderTracker can detect rare founder mutations with high power and negligible false discovery rate. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL6985 GPL8887 GPL6986

49 Samples

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(Submitter supplied) SNP array data from 13 Brazilian childhood adrenocortical tumors (ACTs) were analyzed to detect recurrent copy number changes and highlight potential candidate driver genes.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL6986 GPL6985

19 Samples

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(Submitter supplied) Near-haploid chromosome numbers have been found in less than 1% of cytogenetically reported tumors, but seem to be more common in certain neoplasms including the malignant cartilage-producing tumor chondrosarcoma. By a literature survey of published karyotypes from chondrosarcomas we could confirm that loss of chromosomes resulting in hyperhaploid-hypodiploid cells is common and that these cells may polyploidize. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL8882 GPL6985

16 Samples

Download data: TXT

(Submitter supplied) Hibernomas are benign tumors with morphological features resembling brown fat. They consistently display cytogenetic rearrangements, typically translocations, involving chromosome band 11q13. Here we demonstrate that these aberrations are associated with concomitant deletions of AIP and MEN1, tumor suppressor genes that are located 3 Mb apart and that underlie the hereditary syndromes pituitary adenoma predisposition and multiple endocrine neoplasia type I. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL6984 GPL8882 GPL6985

23 Samples

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(Submitter supplied) Aneuploidy has been well documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening (PGS) in a 24-hour protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy, and distinguishes certain meiotic from mitotic errors. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL6985 GPL8855

130 Samples

Download data: IDAT, XML

(Submitter supplied) Vascular remodeling in pulmonary arterial hypertension (PAH) involves proliferation and migration of endothelial and smooth muscle cells, leading to obliterative vascular lesions. Previous studies have indicated that the endothelial cell proliferation is quasi-neoplastic, with evidence of monoclonality and instability of short DNA microsatellite sequences. To assess whether there is larger scale genomic instability, we performed genome-wide microarray copy number analysis on pulmonary artery endothelial (PAEC) and smooth muscle cells isolated from the lungs of PAH patients. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL5677 GPL6985 GPL8887

24 Samples

Download data: IDAT, TXT

(Submitter supplied) BACKGROUND: Pre-implantation genetic screening (PGS) has been used in an attempt to determine embryonic aneuploidy. Techniques that use new molecular methods to determine the karyotype of an embryo are expanding the scope of PGS. METHODS: We introduce a new method for PGS, termed “Parental Support” (PS), which leverages microarray measurements from parental DNA to “clean” single cell microarray measurements on embryonic cells and explicitly computes confidence in each copy number call. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL6985 GPL8855

622 Samples

Download data: IDAT, XML

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6985 GPL4999

78 Samples

Download data: TXT