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Characterization of adjacent breast tumors using oligonucleotide microarrays.

Unger MA, Rishi M, Clemmer VB, Hartman JL, Keiper EA, Greshock JD, Chodosh LA, Liebman MN, Weber BL - Breast Cancer Res. (2001)

Bottom Line: Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management.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).The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis.

View Article: PubMed Central - PubMed

Affiliation: University of Pennsylvania Cancer Center, Philadelphia, Pennsylvania 19104, USA.

ABSTRACT

Background: Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management. In the present study we evaluated the use of oligonucleotide-based microarray analysis in determining the clonality of tumors by comparing gene expression profiles.

Method: 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.

Results: 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.

Conclusion: Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making.

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Related in: MedlinePlus

Representative log scale scatter plots of average difference values.
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Figure 1: Representative log scale scatter plots of average difference values.

Mentions: The data from the 5A duplicate experiments (5A and 5ADUP) had a pairwise correlation coefficient of 0.995 (Fig. 1). Fifty genes showed a twofold or greater difference in expression between duplicate data sets. Likewise, the 5B duplicate experiments (5B and 5BDUP) had a pairwise correlation coefficient of 0.995, with 36 genes showing a twofold or greater difference in expression (Table 2). None of the 36 genes that were differentially expressed in the 5B/5BDUP experiment were also differentially expressed in the 5A/5ADUP experiment, suggesting that these changes represent random experimental variation.


Characterization of adjacent breast tumors using oligonucleotide microarrays.

Unger MA, Rishi M, Clemmer VB, Hartman JL, Keiper EA, Greshock JD, Chodosh LA, Liebman MN, Weber BL - Breast Cancer Res. (2001)

Representative log scale scatter plots of average difference values.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC57803&req=5

Figure 1: Representative log scale scatter plots of average difference values.
Mentions: The data from the 5A duplicate experiments (5A and 5ADUP) had a pairwise correlation coefficient of 0.995 (Fig. 1). Fifty genes showed a twofold or greater difference in expression between duplicate data sets. Likewise, the 5B duplicate experiments (5B and 5BDUP) had a pairwise correlation coefficient of 0.995, with 36 genes showing a twofold or greater difference in expression (Table 2). None of the 36 genes that were differentially expressed in the 5B/5BDUP experiment were also differentially expressed in the 5A/5ADUP experiment, suggesting that these changes represent random experimental variation.

Bottom Line: Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management.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).The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis.

View Article: PubMed Central - PubMed

Affiliation: University of Pennsylvania Cancer Center, Philadelphia, Pennsylvania 19104, USA.

ABSTRACT

Background: Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management. In the present study we evaluated the use of oligonucleotide-based microarray analysis in determining the clonality of tumors by comparing gene expression profiles.

Method: 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.

Results: 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.

Conclusion: Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making.

Show MeSH
Related in: MedlinePlus