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) Neuroblastoma, like many childhood cancers, exhibits a relative paucity of somatic single nucleotide variants (SNVs). Here, we assess the contribution of structural variation (SV) in neuroblastoma using a combination of whole genome sequencing (WGS; n=135) and single nucleotide polymorphism (SNP) genotyping (n=914) of matched tumor-normal pairs. Our study design provided means for orthogonal validation of SVs as well as validation across genomic platforms. more...

Organism:

Homo sapiens

Type:

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

5 related Platforms

1747 Samples

Download data: IDAT, TXT

(Submitter supplied) Leprosy is a chronic granulomatous disease caused by infection with Mycobacterium leprae. Genetic association studies indicated that leprosy risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but the full number of variants in this region has yet to be elucidated. To identify further susceptibility loci or loss of function variants for this disease, we performed fine-mapping analysis of the MHC region using a Han Chinese reference panel (n= 10,689 patients, 29,948 genetic markers) in the data sets from our previous leprosy studies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL8887

2004 Samples

Download data: TXT, XLSX

(Submitter supplied) Genomic profiling of primary colorectal carcinomas was performed in relation to the spread of CTCs in peripheral and hepatic venous blood, liver metastases, and distant metastases beyond the liver, with the intent to identify specific patterns for the different stages of metastatic spread.

Organism:

Homo sapiens

Type:

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

Platform:

GPL8887

53 Samples

Download data: IDAT, TXT

(Submitter supplied) We genotyped 135 new samples (121 samples from 10 Uralic-speaking and 14 samples from 8 non-Uralic-speaking populations) and combined these data with previously published data to characterize the population structure of Uralic-speaking populations in the context of their geographic neighbours across Eurasia

Organism:

Homo sapiens

Type:

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

4 related Platforms

135 Samples

Download data: TXT

(Submitter supplied) ADP-ribosylation is an important post-translational protein modification that regulates diverse biological processes, controlled by dedicated transferases and hydrolases. Here we show that frequent deletions (~30%) of the MACROD2 mono-ADP-ribosylhydrolase locus in human colorectal cancer (CRC) cause impaired PARP1 transferase activity in a gene dosage-dependent manner. MACROD2 haploinsufficiency alters DNA repair and sensitivity to DNA damage, and results in chromosome instability. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL8887

651 Samples

Download data: TXT

(Submitter supplied) Purpose: Investigation of clonal heterogeneity may be key to understanding mechanisms of therapeutic failure in human cancer. However, little is known on the consequences of therapeutic intervention on the clonal composition of solid tumors. Experimental Design: Here, we used 33 single cell–derived subclones generated from five clinical glioblastoma specimens for exploring intra- and interindividual spectra of drug resistance profiles in vitro. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20886 GPL8887

7 Samples

Download data: IDAT, TXT

(Submitter supplied) With the whole genome SNPs array information, we could evaluate the copy number variation of samples so as to find out specific DNA aberrations in non-Hodgkin lymphma comparing with reactive hyperplasia patients.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL8888 GPL8887

53 Samples

Download data: TXT

(Submitter supplied) The aggressive triple negative breast cancers (TNBCs), which lack estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), comprise a high-risk subset of human breast cancers which remain poorly characterized and lack effective treatments. While meta-analyses have recently suggested the complexity of these tumors, no robust phenotypes have been defined. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL8887 GPL8888

142 Samples

Download data: TXT

(Submitter supplied) Human colorectal cancer (CRC) cell lines are a used widely-used to model system for investigation investigate of tumour biology, experimental therapytherapeutic and biomarkers discovery. However, to what extent these established CRC cell lines represent and maintain the genetic diversity of primary cancers is uncertain. In this study, we analyzed 70 CRC cell lines were analysed for mutations using whole exome sequencing and DNA copy-number using by whole-exome sequencing and SNP microarray profilings, respectively. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL8887

69 Samples

Download data: TXT

(Submitter supplied) We genotyped 322 new samples from 38 Eurasian populations and combined it with previously published data to characterize the population structure of Turkic-speaking populations in the context of their geographic neighbors across Eurasia

Organism:

Homo sapiens

Type:

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

Platforms:

GPL8882 GPL8888 GPL8887

322 Samples

Download data: TXT

(Submitter supplied) A large number of DNA copy number alterations (CNAs) exist in human breast cancers, and thus characterizing the most frequent ones is key to advancing therapeutics because it is likely that these recurrent CNAs contain breast tumor ‘drivers’ (i.e. causal genes). Here, we have comprehensively profiled a large set of human breast tumors and mouse models of mammary cancers using DNA copy number and gene expression microarrays. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome variation profiling by SNP array

Platforms:

GPL4092 GPL8887

201 Samples

Download data: TXT

(Submitter supplied) In colorectal cancer (CRC), chromosomal instability (CIN) is typically studied using comparative-genomic hybridization (CGH) arrays. We studied paired (tumor and surrounding healthy) fresh-frozen tissue from 86 CRC patients using Illumina’s Infinium-based SNP array. This method allowed us to study CIN in CRC, with simultaneous analysis of copy number (CN) and B-allele frequency (BAF), which is a representation of allelic composition. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL8887 GPL13829

172 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

4 related Platforms

68 Samples

Download data: CEL

(Submitter supplied) Low-grade serous ovarian carcinomas are typically Ras-pathway mutated, TP53 wild-type, have limited chromosomal aberration, and are frequently associated with borderline tumors. By contrast, high-grade serous ovarian carcinoma lack Ras-pathway mutations, are invariably TP53 mutated, show widespread genomic change, and are commonly BRCA-pathway disrupted. We sought to identify differences in genomic copy number changes between co-existing borderline and invasive components of serous carcinoma.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL8887

14 Samples

Download data: TXT

(Submitter supplied) SNP array data from 45 adrenocortical carcinomas were used to detect recurrent copy number alterations.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platforms:

GPL8887 GPL13135

45 Samples

Download data

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by high throughput sequencing; SNP genotyping by SNP array; Methylation profiling by genome tiling array; Genome binding/occupancy profiling by array

6 related Platforms

324 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platforms:

GPL8887 GPL8882

122 Samples

Download data

(Submitter supplied) To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS. 67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 67 samples from 51 patients that were genotyped with Illumina Quad610 Beadchip.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL8887

67 Samples

Download data: TXT