Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes

Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 24, 13790-13795, November 20, 2001. Published: 2001.11.12

Arindam Bhattacharjee, William G. Richards, Jane Staunton, Cheng Li, Stefano Monti, Priya Vasa, Christine Ladd, Javad Beheshti, Raphael Bueno, Michael Gillette, Massimo Loda, Griffin Weber, Eugene J. Mark, Eric S. Lander, Wing Wong, Bruce E. Johnson, Todd R. Golub, David J. Sugarbaker, and Matthew Meyerson

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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 sub-classes 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

Keywords: Lung adenocarcinoma

Supplemental Data

Description Link/Filename
Key to scan names datasetA_scans.txt
dfci site for data and supplement http://research.dfci.harvard.edu/meyersonlab/lungca/
Raw data (CEL files) ADENOS part 1 (~53MB) LUNG_scans_ADENO_part1.tar.gz
Raw data (CEL files) ADENOS part 2 (~53MB) LUNG_scans_ADENO_part2.tar.gz
Raw data (CEL files) ADENOS part 3 (~53MB) LUNG_scans_ADENO_part3.tar.gz
Raw data (CEL files) ADENOS part 4 (~54MB) LUNG_scans_ADENO_part4.tar.gz
Raw data (CEL files) ADENOS part 5 (~53MB) LUNG_scans_ADENO_part5.tar.gz
Raw data (CEL files) ADENOS part 6 (~53MB) LUNG_scans_ADENO_part6.tar.gz
Raw data (CEL files) ADENOS part 7 (~54MB) LUNG_scans_ADENO_part7.tar.gz
Raw data (CEL files) ADENOS part 8 (~55MB) LUNG_scans_ADENO_part8.tar.gz
Raw data (CEL files) ADENOS part 9 (~55MB) LUNG_scans_ADENO_part9.tar.gz
Raw data (CEL files) ADENOS part 10 (~53MB) LUNG_scans_ADENO_part10.tar.gz
Raw data (CEL files) Normal Lung (~48MB) LUNG_scans_NORM.tar.gz
Raw data (CEL files) Small Cell (~17MB) LUNG_scans_SMC.tar.gz
Raw data (CEL files) Squamous (~61MB) LUNG_scans_SQ.tar.gz
Raw data (CEL files) Carcinoids (~56MB) LUNG_scans_COID.tar.gz
DatasetA, all genes, rank-inv. scaled, averaged DatasetA_12600gene.txt.gz
All scans, raw AFFY av.diff and A/P vals Lung_DATASETA_scans_noscale.res.gz
Variable genes used to cluster DatasetA DatasetA_3312genesetdescription_sd50.txt
DatasetB, all genes, rank inv. scaled, av'd DatasetB_12600gene_Fig2order.txt.gz
DatasetB, 675 genes DatasetB_675gene.txt.gz