GEO DataSets

(Submitter supplied) Formalin-fixed, paraffin-embedded (FFPE) archival tissue is an important source of DNA material. The most commonly used technique to identify copy number aberrations from chromosomal DNA in tumorigenesis is array comparative genomic hybridization (aCGH). Although copy number analysis using DNA from FFPE archival tissue is challenging, several research groups have reported high quality and reproducible DNA copy number results using aCGH. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10197

11 Samples

Download data: PAIR

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

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL8687 GPL10197

22 Samples

Download data: PAIR, TXT

(Submitter supplied) Formalin-fixed, paraffin-embedded (FFPE) archival tissue is an important source of DNA material. The most commonly used technique to identify copy number aberrations from chromosomal DNA in tumorigenesis is array comparative genomic hybridization (aCGH). Although copy number analysis using DNA from FFPE archival tissue is challenging, several research groups have reported high quality and reproducible DNA copy number results using aCGH. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8687

11 Samples

Download data: TXT

(Submitter supplied) To investigate the cytogenetic and large-scale chromosomal changes in involuted or non-involuted microGISTs using post-whole genome amplification (WGA) FFPE DNA materials

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL13346

21 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Array Comparative Genomic Hybridization (aCGH) is a rapidly evolving technology that still lacks complete standardization. Yet, it is of great importance to obtain robust and reproducible data to enable meaningful multiple hybridization comparisons. Special difficulties arise when aCGH is performed on archival formalin-fixed, paraffin-embedded (FFPE) tissue due to its variable DNA quality. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4560

39 Samples

Download data: TXT

(Submitter supplied) High density SNP microarrays provide insight into the genomic events that occur in diseases like cancer by their capability to measure both LOH and genomic copy numbers. Where currently available methods are restricted to the use of fresh frozen tissue, we now describe the design and validation of copy number measurements using the Illumina BeadArray platform and its application to formalin fixed, paraffin embedded (FFPE) tissue. more...

Organism:

Homo sapiens

Type:

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

4 related Platforms

63 Samples

Download data: CEL, GPR

(Submitter supplied) Pathology archives contain vast resources of clinical material in the form of formalin-fixed paraffin embedded (FFPE) tissue samples. Due to the methods of tissue fixation and storage, the integrity of DNA and RNA available from FFPE tissue is compromised, meaning obtaining informative data regarding epigenetic, genomic and expression alterations can be challenging. Here we have investigated the utility of repairing damaged DNA derived from FFPE tumours prior to single nucleotide polymorphism (SNP) arrays for whole genome DNA copy number analysis.

Organism:

Homo sapiens

Type:

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

Platform:

GPL16483

43 Samples

Download data: TXT

(Submitter supplied) Chromosomal instable colorectal cancer is marked by specific large chromosomal copy number aberrations. Recently, focal aberrations of 3Mb or smaller have been identified as a common phenomenon in cancer. Inherent to their limited size, these aberrations harbour one or few genes. The aim of this study is to identify recurrent focal chromosomal aberrations and their candidate driver genes in a well defined series of stage II colon cancers and assess their potential clinical relevance. more...

Organism:

Homo sapiens

Type:

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

4 related Platforms

61 Samples

Download data: PAIR, TXT

(Submitter supplied) We analysed a cohort of Lifepool IDC cases treated only with wide local excision for genome-wide copy number and loss of heterozygosity using Affymetrix OncoScan® MIP arrays. Cases included IDC (n=4).Benign cases were available for 2 cases. We have analysed copy number calling from the same samples using low-coverage whole genome sequencing in order to investigate the concordance between the two techniques.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL15793 GPL18602

6 Samples

Download data: CEL, OSCHP, TXT

(Submitter supplied) Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), oligonucleotide arrays (185K, Agilent), and two SNP arrays (250K, Affymetrix and 317K, Illumina). Cross-platform comparison revealed 29 concordantly detected CNAs, including known recurrent alterations, which confirmed that all platforms are powerful tools when screening for large aberrations. more...

Organism:

Homo sapiens

Type:

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

4 related Platforms

40 Samples

Download data: CEL, CHP, GPR, TXT

(Submitter supplied) Melanoma is the least common form of skin cancer, but accounts for the most deaths. Dermatopathologists face difficult diganostic determinations with a subset of ambiguous melanoma cases. Copy number variation in melanoma can serve as an additional biomarker to distinguish melanoma from benign melanocytic lesions.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

63 Samples

Download data: CEL, CHP

(Submitter supplied) A study of the relative merits of four leading copy number profiling platforms.

Organism:

Homo sapiens

Type:

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

4 related Platforms

179 Samples

Download data: CEL, PAIR, TXT

(Submitter supplied) The breast tumor microenvironment plays an active role in tumorigenesis. Molecular alterations, including epigenetic modifications to DNA, and changes in RNA and protein expression have been identified in tumor-associated stroma; however, there is considerable debate as to whether the stroma is characterized by genomic instability or whether detection of chromosomal alterations in the breast stroma is a reflection of technological artifact rather than the true genomic content of the tumor microenvironment. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL3720

113 Samples

Download data: CEL, TXT

(Submitter supplied) Characterization of DNA imbalances in a set of 25 MBC samples analyzed by high resolution CGH arrays in order to detect DNA copy number aberrations (CNAs). These results have been then compared with a female breast cancer dataset deposited with the Gene Expression Omnibus.

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL2879 GPL5477

25 Samples

Download data: TXT