GEO DataSets

(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) Objectives: Earlier studies involving a priori gene selection have identified promoter regions deregulated by DNA methylation changes in oral squamous cell cancers (OSCCs) and precancers. Interrogation of global DNA methylation patterns for such specimens has not been reported, though such analyses are needed to uncover novel molecular factors driving disease. Materials and Methods: We evaluated global DNA methylation patterns for 30 biopsies obtained from 10 patients undergoing surgical removal of an OSCC or carcinoma in situ (CIS). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL6480 GPL8490

60 Samples

Download data: TXT

(Submitter supplied) Analysis of DNA from 89 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

86 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) 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) 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) We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridisation (aCGH).

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL14846

72 Samples

Download data: TXT

(Submitter supplied) Array Comparative Genomic Hybridization (CGH) profiling of Oral Sqaumaous Cell Carcinoma (OSCC) was performed to delineate candidate non-random chromosomal loci associated with clinico-pathological parameters. The array CGH hybridizations were performed for 60 OSCC samples with pooled gender matched controls. All tissue samples were collected after obtaining written informed consent.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL10722 GPL4093

60 Samples

Download data: TXT

(Submitter supplied) Lung squamous cell carcinoma (SCC) is thought to arise from premalignant lesions in the airway epithelium, therefore studying these lesions is critical for understanding lung carcinogenesis. We performed RNA sequencing on laser-microdissected representative cell populations along the SCC pathological continuum of patient-matched normal basal cells, premalignant lesions, and tumor cells. We discovered transcriptomic changes and identified genomic pathways altered with initiation and progression of SCC within individual patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

24 Samples

Download data: TXT

(Submitter supplied) Genome-wide screening for regions of genetic gains and losses on nine prostate cancer cell lines (PC3, DU145, LNCaP, CWR22, and derived sublines) was carried out using comparative genomic hybridization on a 35 K longmer oligonucleotide microarray (arrayCGH). Compared to conventional chromosomal CGH more deletions and small regions of gains, particularly in pericentromeric regions and regions next to the telomers, were detected. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL5046

11 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of OSCC tissue samples, oral lichen planus tissue samples and normal controls. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 15 OSCC, 8 lichen planus and 18 control samples.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

41 Samples

Download data: TXT

(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) Chromosomal instability is central to the process of carcinogenesis. The detection of somatic chromosomal alterations in small premalignant lesions genome-wide remains challenging since sample heterogeneity dilutes the aberrant cell information. We introduced an analytic metric termed "delta-θ", and applied this metric to a titrated cancer cell model using a pair of cancer cell line and matched lymphoblastoid cell line. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL16110 GPL8888

57 Samples

Download data: TXT

(Submitter supplied) Our aim is to identify frequent genomic aberrations both in ESCC and esophageal dysplasia, and to discover important copy number-driving genes and microRNAs in ESCC. We carried out array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR and immunohistochemistry (IHC). Integrated analysis was performed to identify genes or microRNAs with copy number-expression correlations.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL17052 GPL8841

75 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) 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

(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

(Submitter supplied) We sought to apply the technologies of gene expression profiling to detect genes significant in the aetiology of cervical carcinoma . We investigated 14 normal (NAD), 11 low grade squamous intrapepithelial lesions (LSIL), 21 high grade squamous intraepithelial lesions (HSIL) and 28 squamous cell carcinomas by Affymetrix GeneChip whole transcriptome profiling. Two SCC cell lines were also included in the cohort. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL571

77 Samples

Download data: CEL