GEO DataSets

(Submitter supplied) BACKGROUND Autofluorescence bronchoscopy (AFB) is a valid strategy for detecting premalignant endobronchial lesions. However, no biomarker can reliably predict lung cancer risk of subjects with AFB-visualized premalignant lesions. Our present study was set out to identify AFB-visualized squamous metaplastic lesions with malignant potential by DNA copy number profiling. METHODS Regular AFB-examinations in 474 subjects at risk of lung cancer identified 6 subjects with SqM lesions at baseline and carcinoma (in situ) at the initial SqM site at follow-up bronchoscopy. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL8841

58 Samples

Download data: TXT

(Submitter supplied) Individuals who present with premalignant endobronchial lesions are considered at high risk of lung cancer. Nonetheless, premalignant lesions behave erratically and only a minority progresses towards lung cancer. Therefore, biomarkers need to be discovered that can aid in assessing an individual’s risk for subsequent cancer to better tailor treatment choices and avoid unnecessary follow-up procedures. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL8841

36 Samples

Download data: TXT

(Submitter supplied) PURPOSE: Bone marrow (BM) is a common homing organ for early disseminated tumor cells (DTC) and their presence can predict the subsequent occurrence of overt metastasis and survival in lung cancer. It is still unclear whether the shedding of DTC from the primary tumor is a random process or a selective release driven by a specific genomic pattern. EXPERIMENTAL DESIGN: DTCs were identified in BM from lung cancer patients by an immunocytochemical cytokeratin assay. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL3055 GPL2819

30 Samples

Download data

(Submitter supplied) We have investigated whether the early dissemination of tumor cells into bone marrow is associated with a specific molecular pattern in primary lung cancer Keywords: primary lung tumor tissue and normal bronchial epithelial tissue

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

19 Samples

Download data: CEL

(Submitter supplied) The majority of patients with squamous cell lung cancer (SCC) die because of metastatic disease. The genomic mechanisms underlying this metastatic behaviour are underexposed. We analyzed a cohort of patients with primary squamous cell carcinoma (SCC) using array-based comparative genomic hybridization (aCGH) to identify which genomic aberrations were related metastatic behaviour. The cohort consisted of 34 patients with a follow-up of at least 5 years, including 15 without any metastases, 8 with metastases in regional lymph nodes only, and 11 with metastases exclusively in distant organs within two years after surgery. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7096

34 Samples

Download data: TXT

(Submitter supplied) High-resolution array-CGH was performed to identify differences in the patterns of genomic imbalances between SCC and AC of non-small cell lung cancer (NSCLC). On a genome-wide profile, SCCs showed higher frequency of gains than ACs (p = 0.067). More specifically, statistically significant differences were observed across the histologic subtypes for gains at 2q14.2, 3q26.2-q29, 12p13.2-p13.33, and 19p13.3, as well as losses at 3p26.2-p26.3, 16p13.11, and 17p11.2 in SCC, and gains at 7q22.1 and losses at 15q22.2-q25.2 occurred in AC (P < 0.05). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL8690

36 Samples

Download data: GPR, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL23126 GPL13534 GPL18281

138 Samples

Download data: CEL, IDAT

(Submitter supplied) Rationale: Lung carcinoma-in-situ (CIS) lesions are the pre-malignant precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those preinvasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. We performed gene expression microarrays on CIS lesions, with a view to deriving a molecular signature predictive of future progression to invasive cancer.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

87 Samples

Download data: IDAT, TXT

(Submitter supplied) Background: Lung carcinoma-in-situ (CIS) lesions are the pre-invasive precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those pre-invasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. Methods: Progressive and regressive CIS lesions were laser-captured and their genome, epigenome and transcriptome interrogated. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

18 Samples

Download data: CEL

(Submitter supplied) Rationale: Lung carcinoma-in-situ (CIS) lesions are the pre-malignant precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those preinvasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. We performed gene expression microarrays on CIS lesions, with a view to deriving a molecular signature predictive of future progression to invasive cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18281

33 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:

GPL8888 GPL16110

57 Samples

Download data: TXT

(Submitter supplied) Reinke's edema (RE) is a laryngeal lesion related to excessive tobacco smoking, voice overuse, and laryngopharyngeal reflux. Although the risk of malignancy is low, RE has been classified among premalignant lesions. Array-based comparative genomic hybridization (aCGH) was used to investigate DNA copy number alterations (CNA) and as a tool to identify markers of risk stratification.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10150

8 Samples

Download data: TXT

(Submitter supplied) DNA copy number variants (CNVs) are associated with the development of complex neurological diseases and disorders including autism spectrum disorder, schizophrenia, Alzheimer’s disease, and Parkinson’s disease. Exposure to multiple environmental chemicals including various heavy metals is suggested as a risk factor in these neurological diseases and disorders, but few studies have addressed if heavy metal exposure can result in spontaneous DNA copy number changes as a genetic mechanism contributing to these disease outcomes. more...

Organism:

Danio rerio

Type:

Genome variation profiling by genome tiling array

Platform:

GPL22921

12 Samples

Download data: TXT, XLSX