GEO DataSets

(Submitter supplied) The molecular etiology underlying TRPS1 loss-of-function in tricho-rhino-phalangeal syndrome (TRPS) remains to be understood. Intriguingly, TRPS1 is also bioinformatically postulated as a breast cancer driver. We report here that TRPS1 is prevalently amplified in breast cancer and promotes breast carcinogenesis. We showed that the tumorigenic potential of TRPS1 is derived from its nucleation of the replication machinery and its enforced replication of H3K9me3-marked heterochromatic regions. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

12 Samples

Download data: CEL, TXT

(Submitter supplied) Medulloblastomas are heterogeneous tumors that collectively represent the most common malignant brain tumor in children. To understand the molecular characteristics underlying their heterogeneity and to identify whether such characteristics represent risk factors for patients with this disease, we performed an integrated genomic analysis of a large series of primary tumors. Identified are six molecular subgroups of medulloblastoma, each with a unique combination of numerical and structural chromosomal aberrations that globally influence mRNA and miRNA expression. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL3720 GPL6801

121 Samples

Download data: CEL, TXT

(Submitter supplied) Since ESCC is a complex and heterogeneous disease, it is increasingly important that analyses combine the evaluation of alterations in DNA, including somatic copy number alterations (SCNA), which distinguished from germ line copy number variants, allelic imbalance and LOH, and RNA, including those that occur in both mRNA and miRNA on the same specimen. Thus, in order to better understand their potential interactions in the development of cancers, in the present study, we studied alterations at DNA level as well as expression of mRNA and target miRNA in tumors and their matched normal tissues from 56 ESCC cases on a candidate tumor suppressor gene CSMD1 to characterize there alterations in this gene for import insights into the cellular detect that cause the complex disease, ESCC.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array

Platform:

GPL6801

40 Samples

Download data: CEL, TXT

(Submitter supplied) Copy number variations were obtained to characterize pancreatic cancer PDX models for tumor research and drug discovery.

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

20 Samples

Download data: CEL, TXT

(Submitter supplied) Affymetrix SNP6.0 array data used to reveal predictive biomarkers of tumour sensitivity to MI-773 . MI-773 is a recently developed small-molecule inhibitor of the Mouse Double Minute 2 (MDM2) proto-oncogene. Here we report an integrative pharmacogenomic study to gain further insights into the therapeutic potential of the compound

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

139 Samples

Download data: CEL, XLSX

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome variation profiling by SNP array; Expression profiling by array

Platforms:

GPL16686 GPL11154 GPL6801

301 Samples

Download data: CEL, CHP, NARROWPEAK, TXT

(Submitter supplied) Dynamic changes to the epigenome are essential regulators of B cell differentiation and, when perturbed, can lead to cancer. We compared three types of mature B cell lymphoma/leukemia (BCL) and normal lymphocytes to identify common and distinct epigenetic perturbations that promote oncogenesis. Purified malignant B cells from 52 patients (18 Follicular, 11 Diffuse Large B Cell, 23 Chronic Lymphocytic Lymphomas) and normal B cell subsets from 28 donor tonsils were subjected to chromatin immunoprecipitation and sequencing (ChIP-seq) for H3K4me1, H3K9/14ac, and H3K27ac; FAIRE-seq for open chromatin; RNA-seq; and genome copy number arrays. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

41 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) In the study we present a multicenter study in which three European diagnostic centres assessed the use of Affymetrix Mapping 500k SNP arrays for molecular karyotyping in patients with mental retardation. Each centre tested DNA from 40 patients with unexplained mental retardation together with their parents. In addition, 38 DNA samples containing known submicroscopic copy number variations (CNVs) were run for validation purposes.

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

49 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL6801 GPL20301 GPL18573

75 Samples

Download data: CEL

(Submitter supplied) The sinoatrial node (SAN) is the primary pacemaker of the heart. The human SAN is poorly understood due to limited primary tissue access and lack of robust in vitro derivation methods. We developed an efficient strategy, using a dual SHOX2:GFP; MYH6:mCherry knock-in reporter line, to generate and purify human pluripotent stem cell-derived SAN cells (hPSC-SAN), displaying molecular and electrophysiological characteristics of bona-fide nodal cells. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

42 Samples

Download data: CEL, TXT

(Submitter supplied) The incidence of breast cancer has been rapidly increasing in East Asia. This is the first study of genome wide copy number of breast cancer in East Asia. We conducted this study to compare the genetic alterations between East and West.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

120 Samples

Download data: CEL, TXT

(Submitter supplied) DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL18637 GPL6801

4 Samples

Download data: CEL, CNCHP, CYCHP

(Submitter supplied) Acute myeloid leukemia (AML) patients carrying complex karyotype or aneuploidies have a very poor prognosis, with a 5-year overall survival lower than 20%. We and others have shown that complex karyotype and aneuploid patients are characterized by high genomic instability, along with defects of DNA damage response genes and, occasionally, by chromothripsis. Chromothripsis frequently occurs in AML (6.6%) and influences patient prognosis and disease biology. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL16131 GPL6801

121 Samples

Download data: CEL, CNCHP, CYCHP

(Submitter supplied) Tetralogy of Fallot (TOF), the most frequent cyanotic congenital heart disease, occurs as a simplex trait of unknown etiology in the majority of cases. Studies of non-Asian populations suggest that approximately 10% of TOF cases carry a de novo rare copy number variant (CNV) thought to underlie the malformation. A genome-wide CNV analysis was performed in 303 TOF and 302 controls of Han Chinese as well as compared to 1,000 common Chinese database and revealed 166 rare CNVs identified in TOF patients with 119 CNVs further evaluated as potential “TOF-specific CNVs”; 98 were validated by qPCR, and 44 CNVs showed positive results on validation (positive rate 46.9%, 44/98). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

466 Samples

Download data: CEL, XLSX

(Submitter supplied) The development of precision medicine strategies requires prior knowledge of the genetic background of the target population. However, despite the availability of data from admixed Americans within large reference population databases, we cannot use these data as a surrogate for that of the Brazilian population. This lack of transferability is mainly due to differences between ancestry proportions of Brazilian and other admixed American populations. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

340 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Autism spectrum disorder (ASD) is an innate neurodevelopmental disorder characterized by impairments in social communication/interaction, repetitive and restrictive behavior. Copy number variation (CNV) is a one of the structural variation of the genomic sequence, including large multiplications and deletions ranging from kb to Mb of DNA. These multiplication-deletion provide genomic diversity, while CNV affects the amount of gene products or transcriptional regulation, and result in strong association with biological process, metabolism and disease. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

192 Samples

Download data: CEL, CHP

(Submitter supplied) Post-radiation sarcomas are rare secondary cancers arising from radiation therapies. To date, few genetic specificities have been described for such malignancies and the oncogenesis of sarcomas with complex genetics (both sporadic and post-radiation) remains largely misunderstood. We performed genomic analyses on both sporadic and post-radiation sarcomas to study their copy-number alterations. This analysis is described in Lesluyes et al. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL6801 GPL16131

133 Samples

Download data: CEL, TSV

(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:

GPL570 GPL6801

89 Samples

Download data: CEL

(Submitter supplied) There is a strong need to develop patient-derived xenograft (PDX) tumor models for studying new treatment options for gastric cancer (GC). With low engraftment success, few collections of GC PDX have been reported and molecular basis of the model establishment remain largely unknown. Here we established n=27 PDX models from n=100 GC tumors and compared their characteristics to GC patient tumors based on the recent work done by ACRG and TCGA, to evaluate the representativeness and relevance of the collection for drug testing. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

62 Samples

Download data: CEL, TXT

(Submitter supplied) Combination of CDK4/6 inhibitors and endocrine therapy has been shown to improve clinical outcome in advanced estrogen receptor-positive breast cancer. However, not all patients will benefit and relapse is inevitable making the identification of new therapeutic strategies/biomarkers of particular importance.

Organism:

Homo sapiens

Type:

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

Platform:

GPL6801

8 Samples

Download data: CEL, CHP