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Open Access 01-12-2008 | Research

Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile

Authors: Ingrid Cifola, Roberta Spinelli, Luca Beltrame, Clelia Peano, Ester Fasoli, Stefano Ferrero, Silvano Bosari, Stefano Signorini, Francesco Rocco, Roberto Perego, Vanessa Proserpio, Francesca Raimondo, Paolo Mocarelli, Cristina Battaglia

Published in: Molecular Cancer | Issue 1/2008

Abstract

Background

Clear cell renal carcinoma (RCC) is the most common and invasive adult renal cancer. For the purpose of identifying RCC biomarkers, we investigated chromosomal regions and individual genes modulated in RCC pathology. We applied the dual strategy of assessing and integrating genomic and transcriptomic data, today considered the most effective approach for understanding genetic mechanisms of cancer and the most sensitive for identifying cancer-related genes.

Results

We performed the first integrated analysis of DNA and RNA profiles of RCC samples using Affymetrix technology. Using 100K SNP mapping arrays, we assembled a genome-wide map of DNA copy number alterations and LOH areas. We thus confirmed the typical genetic signature of RCC but also identified other amplified regions (e.g. on chr. 4, 11, 12), deleted regions (chr. 1, 9, 22) and LOH areas (chr. 1, 2, 9, 13). Simultaneously, using HG-U133 Plus 2.0 arrays, we identified differentially expressed genes (DEGs) in tumor vs. normal samples. Combining genomic and transcriptomic data, we identified 71 DEGs in aberrant chromosomal regions and observed, in amplified regions, a predominance of up-regulated genes (27 of 37 DEGs) and a trend to clustering. Functional annotation of these genes revealed some already implicated in RCC pathology and other cancers, as well as others that may be novel tumor biomarkers.

Conclusion

By combining genomic and transcriptomic profiles from a collection of RCC samples, we identified specific genomic regions with concordant alterations in DNA and RNA profiles and focused on regions with increased DNA copy number. Since the transcriptional modulation of up-regulated genes in amplified regions may be attributed to the genomic alterations characteristic of RCC, these genes may encode novel RCC biomarkers actively involved in tumor initiation and progression and useful in clinical applications.

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Title: Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile
Authors: Ingrid Cifola
Roberta Spinelli
Luca Beltrame
Clelia Peano
Ester Fasoli
Stefano Ferrero
Silvano Bosari
Stefano Signorini
Francesco Rocco
Roberto Perego
Vanessa Proserpio
Francesca Raimondo
Paolo Mocarelli
Cristina Battaglia
Publication date: 01-12-2008
Publisher: BioMed Central
Published in: Molecular Cancer / Issue 1/2008
Electronic ISSN: 1476-4598
DOI: https://doi.org/10.1186/1476-4598-7-6

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