E-MTAB-1133 - Comparative genomic hybridization by array of 121 paired tumor and non-tumor tissue samples from patients with non-small cell lung carcinoma to gain a systems biology insight into the current clinical classification

Status
Last updated on 10 December 2013, released on 11 December 2013
Organism
Homo sapiens
Samples (242)
Array (1)
Protocols (5)
Description
Non-small cell lung cancer (NSCLC), a leading cause of cancer deaths, represents a heterogeneous group of neoplasms, mostly comprising squamous cell carcinoma (SCC), adenocarcinoma (AC) and large-cell carcinoma (LCC). The aim of this study was to gain a systems biology insight into the current clinical classification. Patients and Methods: Comparative genomic hybridization followed by mutational analysis, gene expression and miRNA microarray profiling were performed on 123 paired tumor and non-tumor tissue samples from patients with NSCLC. Using integrated systems biology approaches, we sought to find out if combining data types from different levels of biology would improve clinical assessment of NSCLC. Results: At both DNA, RNA and miRNA levels we could identify molecular markers that discriminated significantly between the various clinicopathological entities of NSCLC. Conclusions: We report proofs of distinct molecular profiles that contribute to distinguishing NSCLC tumor subtypes even in small biopsies. The 121 CGH experiments have been made in dual color with long oligo Agilent Human Genome CGH 244K arrays (design 014693) with a sex apparied DNA reference (Promega). 10 profiles have been discarded due to too much noise.Only 111 profiles have been used in the analysis.
Experiment types
comparative genomic hybridization by array, disease state, reference
Contact
Citation
Integrated molecular portrait of non-small cell lung cancers. Lazar V, Suo C, Orear C, van den Oord J, Balogh Z, Guegan J, Job B, Meurice G, Ripoche H, Calza S, Hasmats J, Lundeberg J, Lacroix L, Vielh P, Dufour F, Lehtiö J, Napieralski R, Eggermont A, Schmitt M, Cadranel J, Besse B, Girard P, Blackhall F, Validire P, Soria JC, Dessen P, Hansson J, Pawitan Y . BMC Medical Genomics 6(1):54 (2013)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MTAB-1133.idf.txt
Sample and data relationshipE-MTAB-1133.sdrf.txt
Raw data (16)Click to browse raw data
Processed data (16)Click to browse processed data
Array designA-AGIL-31.adf.txt
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