DNA copy number analysis in gastrointestinal stromal tumors using gene expression microarrays Journal Article
| Authors: | Antonescu, C. R.; Wu, K.; Guoliang, L. X.; Cao, M.; Turpaz, Y.; Leversha, M. A.; Hubbell, E.; Maki, R. G.; Miyada, C. G.; Pillai, R. |
| Article Title: | DNA copy number analysis in gastrointestinal stromal tumors using gene expression microarrays |
| Abstract: | We report a method, Expression-Microarray Copy Number Analysis (ECNA) for the detection of copy number changes using Affymetrix Human Genome U133 Plus 2.0 arrays, starting with as little as 5 ng input genomic DNA. An analytical approach was developed using DNA isolated from cell lines containing various X-chromosome numbers, and validated with DNA from cell lines with defined deletions and amplifications in other chromosomal locations. We applied this method to examine the copy number changes in DNA from 5 frozen gastrointestinal stromal tumors (GIST). We detected known copy number aberrations consistent with previously published results using conventional or BAC-array CGH, as well as novel changes in GIST tumors. These changes were concordant with results from Affymetrix 100K human SNP mapping arrays. Gene expression data for these GIST samples had previously been generated on U133A arrays, allowing us to explore correlations between chromosomal copy number and RNA expression levels. One of the novel aberrations identified in the GIST samples, a previously unreported gain on 1q21.1 containing the PEX11B gene, was confirmed in this study by FISH and was also shown to have significant differences in expression pattern when compared to a control sample. In summary, we have demonstrated the use of gene expression microarrays for the detection of genomic copy number aberrations in tumor samples. This method may be used to study copy number changes in other species for which RNA expression arrays are available, e.g. other mammals, plants, etc., and for which SNPs have not yet been mapped. |
| Keywords: | human cell; single nucleotide polymorphism; genetic analysis; gastrointestinal stromal tumor; gene amplification; gene expression; gene expression profiling; cell line; sarcoma; chromosome aberration; gene mapping; gene number; correlation analysis; fluorescence in situ hybridization; dna; algorithm; x chromosome; dna microarray; gist; chromosome deletion; chromosome 1q; genomic dna; chromosomal localization; dna isolation; array-based comparative genomic hybridization; copy number change; whole genome amplification; expression microarray copy number analysis |
| Journal Title: | Cancer Informatics |
| Volume: | 6 |
| ISSN: | 1176-9351 |
| Publisher: | Libertas Academica Ltd |
| Date Published: | 2008-01-01 |
| Start Page: | 59 |
| End Page: | 75 |
| Language: | English |
| PROVIDER: | scopus |
| PMCID: | PMC2623304 |
| PUBMED: | 19259404 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 1" - "Export Date: 17 November 2011" - "Source: Scopus" |
Citation Impact
Related MSK Work