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BMC Cancer

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Open Access 01-12-2010 | Research article

Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast

Authors: Lesleyann Hawthorn, Jesse Luce, Leighton Stein, Jenniffer Rothschild

Published in: BMC Cancer | Issue 1/2010

Abstract

Background

A major challenge in the interpretation of genomic profiling data generated from breast cancer samples is the identification of driver genes as distinct from bystander genes which do not impact tumorigenesis. One way to assess the relative importance of alterations in the transcriptome profile is to combine parallel analyses that assess changes in the copy number alterations (CNAs). This integrated analysis permits the identification of genes with altered expression that map within specific chromosomal regions which demonstrate copy number alterations, providing a mechanistic approach to identify the 'driver genes'.

Methods

We have performed whole genome analysis of CNAs using the Affymetrix 250K Mapping array on 22 infiltrating ductal carcinoma samples (IDCs). Analysis of transcript expression alterations was performed using the Affymetrix U133 Plus2.0 array on 16 IDC samples. Fourteen IDC samples were analyzed using both platforms and the data integrated. We also incorporated data from loss of heterozygosity (LOH) analysis to identify genes showing altered expression in LOH regions.

Results

Common chromosome gains and amplifications were identified at 1q21.3, 6p21.3, 7p11.2-p12.1, 8q21.11 and 8q24.3. A novel amplicon was identified at 5p15.33. Frequent losses were found at 1p36.22, 8q23.3, 11p13, 11q23, and 22q13. Over 130 genes were identified with concurrent increases or decreases in expression that mapped to these regions of copy number alterations. LOH analysis revealed three tumors with whole chromosome or p arm allelic loss of chromosome 17. Genes were identified that mapped to copy neutral LOH regions. LOH with accompanying copy loss was detected on Xp24 and Xp25 and genes mapping to these regions with decreased expression were identified. Gene expression data highlighted the PPARα/RXRα Activation Pathway as down-regulated in the tumor samples.

Conclusion

We have demonstrated the utility of the application of integrated analysis using high resolution CGH and whole genome transcript analysis for detecting driver genes in IDC. The high resolution platform allowed a refined demarcation of CNAs and gene expression profiling provided a mechanism to detect genes directly impacted by the CNA. This is the first report of LOH integrated with gene expression in IDC using a high resolution platform.

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The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2407/10/460/prepub

Title: Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast
Authors: Lesleyann Hawthorn
Jesse Luce
Leighton Stein
Jenniffer Rothschild
Publication date: 01-12-2010
Publisher: BioMed Central
Published in: BMC Cancer / Issue 1/2010
Electronic ISSN: 1471-2407
DOI: https://doi.org/10.1186/1471-2407-10-460

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