High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH
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ABSTRACT: Chromosomal regions harboring tumor suppressors and oncogenes are often deleted or amplified. Array comparative genomic hybridization (CGH) detects segmental DNA copy number alterations in tumor DNA relative to a normal control. The recent development of a bacterial artificial chromosome (BAC) array, that spans the human genome in a tiling path manner with >32,000 clones, has facilitated whole genome profiling at an unprecedented resolution. Using this technology, we comprehensively describe and compare the genomes of 28 commonly used non-small cell lung carcinoma cell models, derived from 18 adenocarcinomas, 9 squamous cell carcinomas, and 1 large cell carcinoma. Analysis at such resolution not only provided a detailed genomic alteration template for each of these model cell lines, but revealed novel regions of frequent duplication and deletion. Significantly, a detailed analysis of chromosome 7 identified 6 distinct regions of alterations across this chromosome implicating the presence of multiple novel oncogene loci on this chromosome. As well, a comparison between the squamous and adenocarcinoma cells revealed alterations common to both subtypes, such as the loss of 3p and gain of 5p, in addition to multiple hotspots more frequently associated with only one subtype. Interestingly, chromosome 3q, which is known to be amplified in both subtypes, showed two distinct regions of alteration, one frequently altered in squamous and one more frequent altered in adenocarcinoma. In summary, our data demonstrates the unique information generated by high resolution analysis of NSCLC genomes and uncovers the presence of genetic alterations prevalent in the different NSCLC subtypes. Keywords: array CGH, amplification, segmental copy number, NSCLC, Lung cancer, genetic alterations
ORGANISM(S): Homo sapiens
PROVIDER: GSE2922 | GEO | 2006/02/21
SECONDARY ACCESSION(S): PRJNA92611
REPOSITORIES: GEO
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