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A Method for Detecting Long Non-Coding RNAs with Tiled RNA Expression Microarrays

Author

Listed:
  • Sigrun Helga Lund
  • Daniel Fannar Gudbjartsson
  • Thorunn Rafnar
  • Asgeir Sigurdsson
  • Sigurjon Axel Gudjonsson
  • Julius Gudmundsson
  • Kari Stefansson
  • Gunnar Stefansson

Abstract

Long non-coding ribonucleic acids (lncRNAs) have been proposed as biomarkers in prostate cancer. This paper proposes a selection method which uses data from tiled microarrays to identify relatively long regions of moderate expression independent of the microarray platform and probe design. The method is used to search for candidate long non-coding ribonucleic acids (lncRNAs) at locus 8q24 and is run on three independent experiments which all use samples from prostate cancer patients. The robustness of the method is tested by utilizing repeated copies of tiled probes. The method shows high consistency between experiments that used the same samples, but different probe layout. There also is statistically significant consistency when comparing experiments with different samples. The method selected the long non-coding ribonucleic acid PCNCR1 in all three experiments.

Suggested Citation

  • Sigrun Helga Lund & Daniel Fannar Gudbjartsson & Thorunn Rafnar & Asgeir Sigurdsson & Sigurjon Axel Gudjonsson & Julius Gudmundsson & Kari Stefansson & Gunnar Stefansson, 2014. "A Method for Detecting Long Non-Coding RNAs with Tiled RNA Expression Microarrays," PLOS ONE, Public Library of Science, vol. 9(6), pages 1-9, June.
    • Handle: RePEc:plo:pone00:0099899
    DOI: 10.1371/journal.pone.0099899
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    1. Saravana M. Dhanasekaran & Terrence R. Barrette & Debashis Ghosh & Rajal Shah & Sooryanarayana Varambally & Kotoku Kurachi & Kenneth J. Pienta & Mark A. Rubin & Arul M. Chinnaiyan, 2001. "Delineation of prognostic biomarkers in prostate cancer," Nature, Nature, vol. 412(6849), pages 822-826, August.
    2. Zhijin Wu & Rafael A. Irizarry & Robert Gentleman & Francisco Martinez-Murillo & Forrest Spencer, 2004. "A Model-Based Background Adjustment for Oligonucleotide Expression Arrays," Journal of the American Statistical Association, American Statistical Association, vol. 99, pages 909-917, December.
    3. Adam M. Schmitt & Howard Y. Chang, 2013. "Long RNAs wire up cancer growth," Nature, Nature, vol. 500(7464), pages 536-537, August.
    4. Zhijin Wu & Rafael Irizarry & Robert Gentleman & Francisco Martinez Murillo & Forrest Spencer, 2004. "A Model Based Background Adjustment for Oligonucleotide Expression Arrays," Johns Hopkins University Dept. of Biostatistics Working Paper Series 1001, Berkeley Electronic Press.
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