%0 Journal Article
%T Characterization of adjacent breast tumors using oligonucleotide microarrays
%A Meredith A Unger
%A Mazhar Rishi
%A Virginia B Clemmer
%A Jennifer L Hartman
%A Elizabeth A Keiper
%A Joel D Greshock
%A Lewis A Chodosh
%A Michael N Liebman
%A Barbara L Weber
%J Breast Cancer Research
%D 2001
%I BioMed Central
%R 10.1186/bcr317
%X Total RNA was extracted from two tumors with no apparent physical connection that were located in the right breast of an 87-year-old woman diagnosed with invasive ductal carcinoma (IDC). The RNA was hybridized to the Affymetrix Human Genome U95A Gene Chip£¿ (12,500 known human genes) and analyzed using the Gene Chip Analysis Suite£¿ 3.3 (Affymetrix, Inc, Santa Clara, CA, USA) and JMPIN£¿ 3.2.6 (SAS Institute, Inc, Cary, NC, USA). Gene expression profiles of tumors from five additional patients were compared in order to evaluate the heterogeneity in gene expression between tumors with similar clinical characteristics.The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis. Analysis of gene expression profiles from different individuals, however, generated a pairwise correlation coefficient of 0.710.Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making.Appropriate clinical treatment of an individual with multiple adjacent breast tumors can be difficult to determine. If the tumors originated from the same clone, then they are likely to have common genetic changes and behave in a similar manner. Alternatively, if the tumors are separate primary lesions, then different genetic pathways might have been disrupted and the tumors may require separate treatment strategies [1]. Current methods to detect tumor clonality include methylation-sensitive restriction enzyme digestions and detection of X chromosome polymorphisms, neither of which give an overall genomic assessment of tumors [2].We tested the capabilities of oligonucleotide microarrays in determining tumor clonality. We obtained samples from adjacent tumors from a single individual, and compared the transcriptional profile of each tumor. For comparison, we determined the gene expression profiles of tumors with similar clinical char
%K breast cancer
%K genomics
%K microarrays
%K transcriptional profiling
%K tumor clonality
%U http://breast-cancer-research.com/content/3/5/336