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TAGCNA: A Method to Identify Significant Consensus Events of Copy Number Alterations in Cancer

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  • Xiguo Yuan
  • Junying Zhang
  • Liying Yang
  • Shengli Zhang
  • Baodi Chen
  • Yaojun Geng
  • Yue Wang

Abstract

Somatic copy number alteration (CNA) is a common phenomenon in cancer genome. Distinguishing significant consensus events (SCEs) from random background CNAs in a set of subjects has been proven to be a valuable tool to study cancer. In order to identify SCEs with an acceptable type I error rate, better computational approaches should be developed based on reasonable statistics and null distributions. In this article, we propose a new approach named TAGCNA for identifying SCEs in somatic CNAs that may encompass cancer driver genes. TAGCNA employs a peel-off permutation scheme to generate a reasonable null distribution based on a prior step of selecting tag CNA markers from the genome being considered. We demonstrate the statistical power of TAGCNA on simulated ground truth data, and validate its applicability using two publicly available cancer datasets: lung and prostate adenocarcinoma. TAGCNA identifies SCEs that are known to be involved with proto-oncogenes (e.g. EGFR, CDK4) and tumor suppressor genes (e.g. CDKN2A, CDKN2B), and provides many additional SCEs with potential biological relevance in these data. TAGCNA can be used to analyze the significance of CNAs in various cancers. It is implemented in R and is freely available at http://tagcna.sourceforge.net/.

Suggested Citation

  • Xiguo Yuan & Junying Zhang & Liying Yang & Shengli Zhang & Baodi Chen & Yaojun Geng & Yue Wang, 2012. "TAGCNA: A Method to Identify Significant Consensus Events of Copy Number Alterations in Cancer," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-10, July.
    • Handle: RePEc:plo:pone00:0041082
    DOI: 10.1371/journal.pone.0041082
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    References listed on IDEAS

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    1. Mitchell Guttman & Carolyn Mies & Katarzyna Dudycz-Sulicz & Sharon J Diskin & Don A Baldwin & Christian J Stoeckert Jr. & Gregory R Grant, 2007. "Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays," PLOS Genetics, Public Library of Science, vol. 3(8), pages 1-23, August.
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