High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH

Cathie Garnis, William W. Lockwood, Emily Vucic, Yong Ge, Luc Girard, John D. Minna, Adi F. Gazdar, Stephen Lam, Calum MacAulay, Wan L. Lam

Research output: Contribution to journalArticle

106 Scopus citations

Abstract

Chromosomal regions harboring tumor suppressors and oncogenes are often deleted or amplified. Array comparative genomic hybridization detects segmental DNA copy number alterations in tumor DNA relative to a normal control. The recent development of a bacterial artificial chromosome array, which 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 (NSCLC) cell models, derived from 18 adenocarcinomas (AC), 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 AC 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 1 subtype. Interestingly, chromosome 3q, which is known to be amplified in both subtypes, showed 2 distinct regions of alteration, 1 frequently altered in squamous and 1 more frequently altered in AC. In summary, our data demonstrate the unique information generated by high resolution analysis of NSCLC genomes and uncover the presence of genetic alterations prevalent in the different NSCLC subtypes.

Original languageEnglish (US)
Pages (from-to)1556-1564
Number of pages9
JournalInternational Journal of Cancer
Volume118
Issue number6
DOIs
StatePublished - Mar 15 2006

Keywords

  • Amplification
  • Array CGH
  • Genetic alterations
  • Lung cancer
  • NSCLC
  • Segmental copy number

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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  • Cite this

    Garnis, C., Lockwood, W. W., Vucic, E., Ge, Y., Girard, L., Minna, J. D., Gazdar, A. F., Lam, S., MacAulay, C., & Lam, W. L. (2006). High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. International Journal of Cancer, 118(6), 1556-1564. https://doi.org/10.1002/ijc.21491