Identification of Nine Genomic Regions of Amplification in Urothelial Carcinoma, Correlation with Stage, and Potential Prognostic and Therapeutic Value Journal Article
| Authors: | Chekaluk, Y.; Wu, C. L.; Rosenberg, J.; Riester, M.; Dai, Q.; Lin, S.; Guo, Y.; McDougal, W. S.; Kwiatkowski, D. J. |
| Article Title: | Identification of Nine Genomic Regions of Amplification in Urothelial Carcinoma, Correlation with Stage, and Potential Prognostic and Therapeutic Value |
| Abstract: | We performed a genome wide analysis of 164 urothelial carcinoma samples and 27 bladder cancer cell lines to identify copy number changes associated with disease characteristics, and examined the association of amplification events with stage and grade of disease. Multiplex inversion probe (MIP) analysis, a recently developed genomic technique, was used to study 80 urothelial carcinomas to identify mutations and copy number changes. Selected amplification events were then analyzed in a validation cohort of 84 bladder cancers by multiplex ligation-dependent probe assay (MLPA). In the MIP analysis, 44 regions of significant copy number change were identified using GISTIC. Nine gene-containing regions of amplification were selected for validation in the second cohort by MLPA. Amplification events at these 9 genomic regions were found to correlate strongly with stage, being seen in only 2 of 23 (9%) Ta grade 1 or 1-2 cancers, in contrast to 31 of 61 (51%) Ta grade 3 and T2 grade 2 cancers, p<0.001. These observations suggest that analysis of genomic amplification of these 9 regions might help distinguish non-invasive from invasive urothelial carcinoma, although further study is required. Both MIP and MLPA methods perform well on formalin-fixed paraffin-embedded DNA, enhancing their potential clinical use. Furthermore several of the amplified genes identified here (ERBB2, MDM2, CCND1) are potential therapeutic targets. © 2013 Chekaluk et al. |
| Keywords: | human tissue; gene mutation; mutation; clinical feature; validation process; cancer staging; neoplasm staging; cancer grading; genetic analysis; reproducibility of results; gene; gene targeting; gene amplification; cohort analysis; genetic association; gene function; cancer cell culture; cell line, tumor; bladder cancer; urinary bladder neoplasms; urologic neoplasms; dna; nucleotide sequence; carcinoma; transitional cell carcinoma; gene location; chromosome mapping; genetic identification; dna copy number variations; copy number variation; cancer prognosis; erbb2 gene; neoplasm grading; mdm2 gene; ccnd1 gene; multiplex inversion probe analysis; multiplex ligation dependent probe assay |
| Journal Title: | PLoS ONE |
| Volume: | 8 |
| Issue: | 4 |
| ISSN: | 1932-6203 |
| Publisher: | Public Library of Science |
| Date Published: | 2013-04-04 |
| Start Page: | e60927 |
| Language: | English |
| PROVIDER: | scopus |
| PMCID: | PMC3617176 |
| PUBMED: | 23593348 |
| DOI: | 10.1371/journal.pone.0060927 |
| DOI/URL: | |
| Notes: | --- - "Export Date: 1 May 2013" - ":doi 10.1371/journal.pone.0060927" - "Source: Scopus" |
