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Links from GEO DataSets

Items: 20

1.

Copy number alteration burden is a pan-cancer prognostic factor associated with metastasis and death in conservatively treated prostate cancer: TAPG1 CNA cohort aCGH data

(Submitter supplied) The level of copy number alteration (CNA), or CNA burden, in cancer genomes is associated with recurrence and metastasis in prostate cancer. As clinical genomic analysis of tumors and tumor biopsies becomes widespread, there is a growing need to understand the prognostic factors captured by genomic features, especially in prostate cancer where conservative treatment approaches are increasingly common. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by genome tiling array
Platforms:
GPL10152 GPL10123
107 Samples
Download data: TXT
Series
Accession:
GSE103665
ID:
200103665
2.

Copy number alteration burden predicts prostate cancer relapse: Agilent 1M aCGH data for human primary prostate cancer samples

(Submitter supplied) Prostate cancer is the most common malignancy in men. Yet, the modest benefit of treatment highlights the unmet need for prognostic biomarkers in prostate cancer (1). Few large prostate oncogenome resources currently exist that combine the molecular and clinical outcome data necessary for prognostic discovery. To determine the extent to which genomic aberrations reflect the risk of prostate cancer-specific outcomes, we profiled more than 100 primary prostate cancers with long-term follow-up for genome-wide copy number alterations (CNA). more...
Organism:
Homo sapiens
Type:
Genome variation profiling by genome tiling array
Platform:
GPL8737
104 Samples
Download data: TXT
Series
Accession:
GSE54691
ID:
200054691
3.

Expression and SNP array data for oral squamous cell carcinoma

(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; SNP genotyping by SNP array
Platforms:
GPL5175 GPL6801
201 Samples
Download data: CEL, CHP
Series
Accession:
GSE25104
ID:
200025104
4.

Affymetrix SNP array data for oral squamous cell carcinoma

(Submitter supplied) In order to identify biomarkers that contribute to genetic causes of OSCC, we attempt to identify copy number variation regions (CNV) in patients with OSCC. We identified and confirmed the clinical significance of amplification regions scattered from 8q22.2 to 8q24.3.
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array; SNP genotyping by SNP array
Platform:
GPL6801
122 Samples
Download data: CEL, CHP, TXT
Series
Accession:
GSE25103
ID:
200025103
5.

Affymetrix SNP 6.0 data for analysis of esophageal adenocarcinoma samples

(Submitter supplied) Esophageal adenocarcinoma is characterized by complex chromosomal alterations. Tumors were evaluated to identify regions of recurrent copy gains and losses and to determine the prognositic significance of the degree of segmental aneuploidy as measured by SNP array.
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array; SNP genotyping by SNP array
Platform:
GPL6801
82 Samples
Download data: CEL, CHP
Series
Accession:
GSE49396
ID:
200049396
6.

Mammary Tissue: aCGH of primary (IGF-IR induced) and recurrent (IGF-IR independent) mammary tumors from MTB-IGFIR mice

(Submitter supplied) Tumor recurrence represents a significant clinical challenge in the treatment and management of breast cancer. To investigate whether copy number aberrations (CNAs) facilitate the re-emergence of tumor growth from residual disease we performed array comparative genomic hybridization (aCGH) on primary and recurrent mammary tumors from an inducible mouse model of type-I insulin-like growth factor receptor (IGF-IR) driven breast cancer. more...
Organism:
Mus musculus
Type:
Genome variation profiling by genome tiling array
Platform:
GPL15076
19 Samples
Download data: TXT
Series
Accession:
GSE120186
ID:
200120186
7.

Mammary Tissue: Wild type mammary glands vs IGF-IR induced mammary tumors vs IGF-IR independent tumors

(Submitter supplied) Molecular profiling was used to classify mammary tumors that develop in MTB-IGFIR transgenic mice. It was determined that the primary mammary tumors (PMT), which develop due to elevated expression of the type I insulin-like growth factor receptor (IGF-IR) in mammary epithelial cells, most closely resemble murine tumors with basal-like or mixed gene expression profiles and with human basal-like breast cancers. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL7202
28 Samples
Download data: TXT
Series
Accession:
GSE32152
ID:
200032152
8.

Prostate cancer stratification using molecular profiles [Stockholm genotype]

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumor, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array
Platform:
GPL6801
180 Samples
Download data: CEL, TXT
Series
Accession:
GSE73076
ID:
200073076
9.

Prostate cancer stratification using molecular profiles [CamCap genotype third set]

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array
Platform:
GPL16104
7 Samples
Download data: IDAT, TXT
Series
Accession:
GSE73012
ID:
200073012
10.

Prostate cancer stratification using molecular profiles [CamCap genotype second set]

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array
Platform:
GPL20641
28 Samples
Download data: IDAT, TXT
Series
Accession:
GSE73011
ID:
200073011
11.

Prostate cancer stratification using molecular profiles [CamCap genotype first set]

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array
Platform:
GPL16104
300 Samples
Download data: IDAT, TXT
Series
Accession:
GSE71965
ID:
200071965
12.

Prostate cancer stratification using molecular profiles

(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
808 Samples
Download data: CEL, IDAT
Series
Accession:
GSE70770
ID:
200070770
13.

Prostate cancer stratification using molecular profiles [Stockholm ExpressionArray]

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
94 Samples
Download data: TXT
Series
Accession:
GSE70769
ID:
200070769
14.

Prostate cancer stratification using molecular profiles [CamCap ExpressionArray]

(Submitter supplied) Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behavior, and compared with either CNA or transcriptomics alone. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
199 Samples
Download data: TXT
Series
Accession:
GSE70768
ID:
200070768
15.

Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer

(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
Series
Accession:
GSE31645
ID:
200031645
16.

Intratumor genomic heterogeneity in stage II colon cancer

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array; Other
Platforms:
GPL21558 GPL15520
128 Samples
Download data: CEL, OSCHP, VCF
Series
Accession:
GSE172191
ID:
200172191
17.

Targeted Next-Generation Sequencing for profiling frequently mutated genes in early-stage colon cancer

(Submitter supplied) Intratumor heterogeneity fosters the evolution of the genome leading to metastatic progress and therapy resistance. Here, we investigate the relative contribution of genomic heterogeneity involving mutations and CNAs as prognostic and predictive determinants for disease recurrence in early-stage colon cancer. We combined targeted next-generation sequencing (NGS) and SNP arrays on a retrospective cohort of untreated stage II colon cancer patients to assess the association of genomic subclonality with time to recurrence (TTR).
Organism:
Homo sapiens
Type:
Other
Platform:
GPL15520
44 Samples
Download data: VCF
Series
Accession:
GSE172190
ID:
200172190
18.

Affymetrix OncoScan SNP arrays for profiling copy-number alterations (CNAs) and loss-of-heterozygosity (LOH) in colon cancer

(Submitter supplied) Intratumor heterogeneity fosters the evolution of the genome leading to metastatic progress and therapy resistance . Here, we investigate the relative contribution of tumor aneuploidy and genomic heterogeneity involving CNAs and mutational events as prognostic and predictive determinants for disease recurrence in early-stage colon cancer patients. We combined SNP arrays, targeted next-generation sequencing, fluorescence in situ hybridization and inmunohistochemistry on a retrospective cohort of 84 untreated stage II colon cancer patients. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array
Platform:
GPL21558
84 Samples
Download data: CEL, OSCHP
Series
Accession:
GSE171777
ID:
200171777
19.

Expression data from fine-needle aspiration biopsies of breast cancer metastases from different anatomical sites

(Submitter supplied) To determine whether breast cancer molecular subtypes and tumor characteristics with demonstrated significance in a primary tumor setting can also confer clinically relevant information in breast cancer metastases. We assessed previously published gene expression modules of seven biological processes and the intrinsic subtypes (PAM50). The translational aspect of the Swedish randomized TEX trial included 112 patients with at least one biopsy from morphologically confirmed loco-regional or distant breast cancer metastasis diagnosed from December 2002 until June 2007. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10379
120 Samples
Download data: CEL
Series
Accession:
GSE56493
ID:
200056493
20.

A nested case-control study to investigate drivers for metastatic disease in breast cancer

(Submitter supplied) The purpose of this study was to improve prediction of patients at high-risk for metastatic disease utilizing a nested case-control design that uniquely enables enrichment for relevant phenotypes. We identified all women diagnosed with primary breast cancer from January 1, 1997, to December 31, 2005, in the Stockholm health care region. Patients developing distant metastatic disease (cases) were selected and controls (free from distant disease) were randomly matched by adjuvant therapy, age and calendar period at diagnosis. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10379
623 Samples
Download data: CEL
Series
Accession:
GSE48091
ID:
200048091
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