title: Genome position and gene amplification.
abstract: BACKGROUND
  Amplifications, regions of focal high-level copy number change, lead to overexpression of oncogenes or drug resistance genes in tumors. Their presence is often associated with poor prognosis; however, the use of amplification as a mechanism for overexpression of a particular gene in tumors varies. To investigate the influence of genome position on propensity to amplify, we integrated a mutant form of the gene encoding dihydrofolate reductase into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells.
  
  
  RESULTS
  We observed site-specific differences in methotrexate sensitivity, amplicon organization and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate-sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site.
  
  
  CONCLUSIONS
  These studies suggest that genome context together with the particular challenges to genome stability experienced during the progression to cancer contribute to the propensity to amplify a specific oncogene or drug resistance gene, whereas the overall functional response to drug (or other) challenge may be independent of the genomic location of an oncogene.
authors.affiliation: Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA.
authors.forename: Pavla
authors.initials: P
authors.lastname: Gajduskova
authors.forename: Antoine M
authors.initials: AM
authors.lastname: Snijders
authors.forename: Serena
authors.initials: S
authors.lastname: Kwek
authors.forename: Ritu
authors.initials: R
authors.lastname: Roydasgupta
authors.forename: Jane
authors.initials: J
authors.lastname: Fridlyand
authors.forename: Taku
authors.initials: T
authors.lastname: Tokuyasu
authors.forename: Daniel
authors.initials: D
authors.lastname: Pinkel
authors.forename: Donna G
authors.initials: DG
authors.lastname: Albertson
mesh_terms: D045744:Cell Line, Tumor; D005784:Gene Amplification / Q000187:drug effects; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008727:Methotrexate / Q000494:pharmacology; D013762:Tetrahydrofolate Dehydrogenase / Q000235:genetics
chemical_list: D013762:Tetrahydrofolate Dehydrogenase; D008727:Methotrexate