GEO DataSets

(Submitter supplied) Oral potentially malignant disorders (OPMDs) may precede oral squamous cell carcinoma (OSCC). Early detection of OPMDs has a crucial role in OSCC prevention. DNA aneuploidy and chromosomal aberrations are markers of genomic DNA damage and chromosomal instability (CIN), which is involved in cancer development. We explored the relationship among genomic DNA copy number aberrations (CNAs), histological diagnosis and DNA aneuploidy in OPMDs/OSCCs. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL9075 GPL10150

151 Samples

Download data: TXT

(Submitter supplied) The aim of the study was to address the concept of field cancerization in oral cancer. The presence of genomic aberrations, indicative of chromosomal instability (CIN), in oral distant fields (ODFs) of visually normal and non-dysplastic mucosa at the mirror image from concomitant oral potentially malignant lesions (OPMLs) was investigated. This pilot study comprised 16 OPMLs (8 without dysplasia, nd-OPMLs; 8 with dysplasia, d-OPMLs) and 16 ODFs. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4093

32 Samples

Download data: TXT

(Submitter supplied) The mucosae of the oral cavity are different at the histological level but are all exposed to common genotoxic agents. As a result of this exposure, changes in the mucosal epithelia develop giving rise to Oral Potentially Malignant Lesions (OPMLs), which with time may in turn progress to Oral Squamous Cell Carcinomas (OSCCs). Therefore, much effort should be devoted to identify features able to predict the likeliness of progression associated with an OPML. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4093

35 Samples

Download data: TXT

(Submitter supplied) DNA aneuploid sublines in sporadic colorectal cancers (CRCs) are quite frequent (about 85%) and likely the consequence of chromosomal instability and DNA copy number aberrations (CNAs). In order to gain insight into the mechanisms of the diploid-aneuploid transition in CRCs, we compared the CNA status in both diploid and aneuploid sublines. We used fresh/frozen material from 17 aneuploid CRCs, which was separated into 17 DNA diploid and 17 aneuploid sublines using enrichment of the epithelial component by multiparameter flow cytometry and sorting. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8687

34 Samples

Download data: TXT

(Submitter supplied) In this study, we investigated CNAs of 40 tumor samples from 25 patients, including 15 metastatic primary tumor (MPT), paired neck lymph-node metastasis (LNM) and 10 non-metastatic primary tumor (NMPT), by 44k oligonucleotide-based array comparative genomic hybridization (array CGH).

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL5477

42 Samples

Download data: TXT

(Submitter supplied) Genome-wide profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL22687

75 Samples

Download data: TXT

(Submitter supplied) Clinically evident oral lesions, oral epithelial dysplasia, precede development of oral squamous cell carcinomas (SCC) and are considered to transform to cancer by acquisition of genetic or epigenetic alterations. Here, we show that, +3q24-qter, -8pter-p23.1, +8q12-q24.2 and +20 are early events identifying two pathways to oral cancers that differ in clinical behavior. One or more of these copy number aberrations is present in the major subgroup (3q8pq20 subtype, 75-80% of lesions) that develops with chromosomal instability and risk for metastasis, while they are absent from the smaller and chromosomally stable non-3q8pq20 subgroup (20-25% of lesions) associated with low risk for metastasis. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL6359 GPL4421 GPL4999

168 Samples

Download data: TXT

(Submitter supplied) Analysis of DNA from 94 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL2043 GPL2616

94 Samples

Download data: TXT

(Submitter supplied) Primary tumor heterogeneity can significantly affect the genetic profile of clones at metastatic sites. In order to understand the mechanisms underlying metastasis, we compared the genetic profile of paired primary tumor (PT) and metastatic lymph node (MLN) samples obtained from individual patients.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18602

40 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. BACKGROUND: Cell lines have been developed for modeling cancer and cancer progression. The molecular background of these cell lines is often unknown to those using them to model disease behaviors. As molecular alterations are the ultimate drivers of cell phenotypes, having an understanding of the molecular make-up of these systems is critical for understanding the disease biology modeled. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL18947 GPL6480

18 Samples

Download data: TXT

(Submitter supplied) Profiling of copy number mutations in commonly used non-cancerous oral cell lines

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL18947

8 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Cell lines have been developed for modeling cancer and cancer progression. The molecular background of these cell lines is often unknown to those using them to model disease behaviors. As molecular alterations are the ultimate drivers of cell phenotypes, having an understanding of the molecular make-up of these systems is critical for understanding the disease biology modeled. METHODS: Six immortalized normal, one immortalized dysplasia, one self-immortalized dysplasia, and two primary normal cell lines derived from oral tissues were analyzed for DNA copy number changes and changes in both mRNA and miRNA expression using SMRT-v.2 genome-wide tiling comparative genomic hybridization arrays, Agilent Whole Genome 4x44k expression arrays, and Exiqon V2.M-RT-PCR microRNA Human panels. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

10 Samples

Download data: TXT

(Submitter supplied) The identification of cancer drivers is a major goal of current cancer research. Finding driver genes within large chromosomal events is especially challenging because such alterations encompass many genes. Previously, we demonstrated that zebrafish malignant peripheral nerve sheath tumors (MPNSTs) are highly aneuploid, much like human tumors. In this study, we examined 147 zebrafish MPNSTs by massively parallel sequencing and identified both large and focal copy number alterations (CNAs). more...

Organism:

Danio rerio

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL15583

294 Samples

Download data: TXT

(Submitter supplied) Diploid human cell lines were treated with aphidicolin as a model to see how DNA replication stress affects the genome, by identifying which copy number alterations appear in the first cell cycle. RNAseq was used to see whether there is any link between loci with recurrent CNAs and gene transcription in the genes located there.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array; Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL5175 GPL13534 GPL14943

132 Samples

Download data: CEL, TXT

(Submitter supplied) Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

43 Samples

Download data: CEL

(Submitter supplied) Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL14943

43 Samples

Download data: TXT

(Submitter supplied) Oral cavity squamous cell carcinoma (OSCC) is a disease with extensive morbidity and mortality and few useful molecular targets. Multiplatform integrated genomic analysis was performed in order to identify genomic drivers and molecularly discernible tumor subtypes. mRNA, miRNA and methylation data are all submitted to GEO

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

46 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; Other

Platforms:

GPL21558 GPL15520

128 Samples

Download data: CEL, OSCHP, VCF

(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