Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate Cancer
Prostate cancer is a clinically and biologically heterogeneous disease. Deregulation of splice variants has been shown to contribute significantly to this complexity. High-throughput technologies such as oligonucleotide microarrays allow for the detection of transcripts that play a role in disease p...
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doaj-89a870d18bb143b793d045d4f2179d5d2020-11-25T00:02:57ZengHindawi LimitedJournal of Oncology1687-84501687-84692012-01-01201210.1155/2012/541353541353Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate CancerNicholas Erho0Christine Buerki1Timothy J. Triche2Elai Davicioni3Ismael A. Vergara4Department of Research and Development, GenomeDx Biosciences Inc., Vancouver, BC, V6J 1J8, CanadaDepartment of Research and Development, GenomeDx Biosciences Inc., Vancouver, BC, V6J 1J8, CanadaDepartment of Research and Development, GenomeDx Biosciences Inc., Vancouver, BC, V6J 1J8, CanadaDepartment of Research and Development, GenomeDx Biosciences Inc., Vancouver, BC, V6J 1J8, CanadaDepartment of Research and Development, GenomeDx Biosciences Inc., Vancouver, BC, V6J 1J8, CanadaProstate cancer is a clinically and biologically heterogeneous disease. Deregulation of splice variants has been shown to contribute significantly to this complexity. High-throughput technologies such as oligonucleotide microarrays allow for the detection of transcripts that play a role in disease progression in a transcriptome-wide level. In this study, we use a publicly available dataset of normal adjacent, primary tumor, and metastatic prostate cancer samples (GSE21034) to detect differentially expressed coding and non-coding transcripts between these disease states. To achieve this, we focus on transcript-specific probe selection regions, that is, those probe sets that correspond unambiguously to a single transcript. Based on this, we are able to pinpoint at the transcript-specific level transcripts that are differentially expressed throughout prostate cancer progression. We confirm previously reported cases and find novel transcripts for which no prior implication in prostate cancer progression has been made. Furthermore, we show that transcript-specific differential expression has unique prognostic potential and provides a clinically significant source of biomarker signatures for prostate cancer risk stratification. The results presented here serve as a catalog of differentially expressed transcript-specific markers throughout prostate cancer progression that can be used as basis for further development and translation into the clinic.http://dx.doi.org/10.1155/2012/541353 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Nicholas Erho Christine Buerki Timothy J. Triche Elai Davicioni Ismael A. Vergara |
spellingShingle |
Nicholas Erho Christine Buerki Timothy J. Triche Elai Davicioni Ismael A. Vergara Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate Cancer Journal of Oncology |
author_facet |
Nicholas Erho Christine Buerki Timothy J. Triche Elai Davicioni Ismael A. Vergara |
author_sort |
Nicholas Erho |
title |
Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate Cancer |
title_short |
Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate Cancer |
title_full |
Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate Cancer |
title_fullStr |
Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate Cancer |
title_full_unstemmed |
Transcriptome-Wide Detection of Differentially Expressed Coding and Non-Coding Transcripts and Their Clinical Significance in Prostate Cancer |
title_sort |
transcriptome-wide detection of differentially expressed coding and non-coding transcripts and their clinical significance in prostate cancer |
publisher |
Hindawi Limited |
series |
Journal of Oncology |
issn |
1687-8450 1687-8469 |
publishDate |
2012-01-01 |
description |
Prostate cancer is a clinically and biologically heterogeneous disease. Deregulation of splice variants has been shown to contribute significantly to this complexity. High-throughput technologies such as oligonucleotide microarrays allow for the detection of transcripts that play a role in disease progression in a transcriptome-wide level. In this study, we use a publicly available dataset of normal adjacent, primary tumor, and metastatic prostate cancer samples (GSE21034) to detect differentially expressed coding and non-coding transcripts between these disease states. To achieve this, we focus on transcript-specific probe selection regions, that is, those probe sets that correspond unambiguously to a single transcript. Based on this, we are able to pinpoint at the transcript-specific level transcripts that are differentially expressed throughout prostate cancer progression. We confirm previously reported cases and find novel transcripts for which no prior implication in prostate cancer progression has been made. Furthermore, we show that transcript-specific differential expression has unique prognostic potential and provides a clinically significant source of biomarker signatures for prostate cancer risk stratification. The results presented here serve as a catalog of differentially expressed transcript-specific markers throughout prostate cancer progression that can be used as basis for further development and translation into the clinic. |
url |
http://dx.doi.org/10.1155/2012/541353 |
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