Transcriptomics

Dataset Information

24

Expression data of different histological subgroups of non-small cell lung cancer in two patient populations with different survival outcomes


ABSTRACT: Hypothesis: Non-small cell lung cancer (NSCLC) is characterized by a multitude of genetic aberrations with unknown clinical impact. In this study, we aimed to identify gene copy number changes that correlate with clinical outcome in NSCLC. To maximize the chance to identify clinically relevant events, we applied a strategy involving two prognostically extreme patient groups. Results: Genetic aberrations were strongly associated with tumor histology. In adenocarcinoma (n=50), gene copy number gains on chromosome 8q21-q24.3 (177 genes) were more frequent in long-term survivors. In squamous cell carcinoma (n=28), gains on chromosome 14q23.1-24.3 (133 genes) were associated with shorter survival, whereas losses in a neighboring region, 14q31.1-32.33 (110 genes), correlated with favorable outcome. In accordance with copy number gains and losses, mRNA expression levels of corresponding genes were increased or decreased, respectively. Conclusion: Comprehensive tumor profiling permits the integration of genomic, histologic and clinical data. We identified gene copy number gains and losses, with corresponding changes in mRNA levels, that were associated with prognosis in adenocarcinoma and squamous cell carcinoma of the lung. Short-term (<20 months; n=53) and long-term survivors (>58 months; n=47) were selected from a clinically well-characterized NSCLC patient cohort with available fresh-frozen tumor specimens. The samples were analyzed using array-based gene expression profiling. The molecular data was combined with information on clinical parameters.

REANALYSED by: E-GEOD-28571

ORGANISM(S): Homo sapiens  

SUBMITTER: Patrick Micke   Karolina Edlund  Hanna G√∂ransson  Johan Botling  Kristina Lamberg  Anders Isaksson  Andrew Thomas  Michael Bergqvist  Lars Holmberg  Gunnar Myrdal  Simon Ekman  Lena Scheibenflug  Anders Berglund  Fredrik Nyberg  Mats Lambe 

PROVIDER: E-GEOD-28571 | ArrayExpress | 2011-10-27

SECONDARY ACCESSION(S): GSE28571PRJNA143017

REPOSITORIES: GEO, ArrayExpress

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Publications

Gene copy number aberrations are associated with survival in histologic subgroups of non-small cell lung cancer.

Micke Patrick P   Edlund Karolina K   Holmberg Lars L   Kultima Hanna Göransson HG   Mansouri Larry L   Ekman Simon S   Bergqvist Michael M   Scheibenflug Lena L   Lamberg Kristina K   Myrdal Gunnar G   Berglund Anders A   Andersson Annsofie A   Lambe Mats M   Nyberg Fredrik F   Thomas Andrew A   Isaksson Anders A   Botling Johan J  

Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 20111101 11


INTRODUCTION: Non-small cell lung cancer (NSCLC) is characterized by a multitude of genetic aberrations with unknown clinical impact. In this study, we aimed to identify gene copy number changes that correlate with clinical outcome in NSCLC. To maximize the chance to identify clinically relevant events, we applied a strategy involving two prognostically extreme patient groups. METHODS: Short-term (<20 month; n = 53) and long-term survivors (>58 month; n = 47) were selected from a clinically well  ...[more]

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