Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

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Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

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dc.contributor.author Oudes, Asa J. en_US
dc.contributor.author Roach, Jared C. en_US
dc.contributor.author Walashek, Laura S. en_US
dc.contributor.author Eichner, Lillian J.. en_US
dc.contributor.author True, Lawrence D. en_US
dc.contributor.author Vessella, Robert L. en_US
dc.contributor.author Liu, Alvin Y. en_US
dc.date.accessioned 2010-05-06T20:07:43Z
dc.date.available 2010-05-06T20:07:43Z
dc.date.issued 2005 en_US
dc.identifier.citation Oudes A, Roach J, Walashek L, et al. Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression. BMC Cancer. 2005;5(1):86. en_US
dc.identifier.other 10.1186/1471-2407-5-86 en_US
dc.identifier.uri http://www.biomedcentral.com/1471-2407/5/86 en_US
dc.identifier.uri http://hdl.handle.net/1773/15859
dc.description.abstract Background: Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Methods: Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Results: Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis. Conclusion: Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases. en_US
dc.description.sponsorship NIH grants CA85859, DK63630, and CA98699. en_US
dc.language.iso en_US en_US
dc.title Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression en_US
dc.type Article en_US


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