Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

CaArray_meyer-00191: Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses

ABSTRACT: We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct subclasses of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients. meyer-00191 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HG_U95Av2 Organism: Homo sapiens (ncbitax) Material Types: total RNA, synthetic_RNA, organism_part, whole_organism Disease States: lung cancer, Normal

ORGANISM(S): Homo sapiens

DISEASE(S): Lung Cancer

SUBMITTER: Mervi Heiskanen

PROVIDER: E-GEOD-83227 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.

Bhattacharjee A A Richards W G WG Staunton J J Li C C Monti S S Vasa P P Ladd C C Beheshti J J Bueno R R Gillette M M Loda M M Weber G G Mark E J EJ Lander E S ES Wong W W Johnson B E BE Golub T R TR Sugarbaker D J DJ Meyerson M M

Proceedings of the National Academy of Sciences of the United States of America 20011113 24

We have generated a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, we analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct subclasses of lung adenocarcinoma. Among these were tumors with high relative expression of neuroe ...[more]

PMID: 11707567

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Project description:A key step in bringing gene expression data into clinical practice is the conduct of large studies to confirm preliminary models. The performance of such confirmatory studies and the transition to clinical practice requires that microarray data from different laboratories are comparable and reproducible. We designed a study to assess the comparability of data from four laboratories that will conduct a larger microarray profiling confirmation project in lung adenocarcinomas. To test the feasibility of combining data across laboratories, frozen tumor tissues, cell line pellets, and purified RNA samples were analyzed at each of the four laboratories. Samples of each type and several subsamples from each tumor and each cell line were blinded before being distributed. The laboratories followed a common protocol for all steps of tissue processing, RNA extraction, and microarray analysis using Affymetrix Human Genome U133A arrays. High within-laboratory and between-laboratory correlations were observed on the purified RNA samples, the cell lines, and the frozen tumor tissues. Intraclass correlation within laboratories was only slightly stronger than between laboratories, and the intraclass correlation tended to be weakest for genes expressed at low levels and showing small variation. Finally, hierarchical cluster analysis revealed that the repeated samples clustered together regardless of the laboratory in which the experiments were done. The findings indicate that under properly controlled conditions it is feasible to perform complete tumor microarray analysis, from tissue processing to hybridization and scanning, at multiple independent laboratories for a single study. dobbi-00100 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HG-U133A Organism: Homo sapiens (ncbitax) Tissue Sites: Kidney, Lung, Stomach, Uterus, Liver, Lymphoid tissue, Ovary, Skin, Adrenal Gland, Lymph_Node Material Types: cell, nuclear_RNA, synthetic_RNA, organism_part, total_RNA Disease States: Recurrent Renal Cell Carcinoma, Squamous Cell Carcinoma,Conventional_Clear_Cell_Renal_Cell_Carcinoma,Gastrointestinal_Stromal_Tumor, Lung_Adenocarcinoma, Leiomyoma, Non neoplastic liver with cirrosis, Stomach Adenocarcinoma, Large Cell Lymphoma, Ovarian Adenocarcinoma, Melanoma, Malignant G1 Stromal Tumor, Adrenal Cortical Adenoma, Metastatic Renal Cell Carcinoma, Malignant Melanoma

Dataset Information

CaArray_meyer-00191: Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses

Publications

Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.

Similar Datasets

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