Copy-number-aware differential analysis of quantitative DNA sequencing data
- Mark D. Robinson1,2,3,7,
- Dario Strbenac3,
- Clare Stirzaker3,6,
- Aaron L. Statham3,
- Jenny Song3,
- Terence P. Speed4,5 and
- Susan J. Clark3,6
- 1Institute of Molecular Life Sciences,
- 2SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland;
- 3Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia;
- 4Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne 3052, Victoria, Australia;
- 5Department of Medical Biology, University of Melbourne, 3050, Victoria, Australia;
- 6St. Vincent's Clinical School, University of New South Wales, Sydney 2010, New South Wales, Australia
Abstract
Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities and can therefore bias differential detection results. We have developed a flexible approach called ABCD-DNA (affinity-based copy-number-aware differential quantitative DNA sequencing analyses) that integrates CNV and other systematic factors directly into the differential enrichment engine.
Footnotes
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↵7 Corresponding author
E-mail mark.robinson{at}imls.uzh.ch
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.139055.112.
Freely available online through the Genome Research Open Access option.
- Received February 13, 2012.
- Accepted August 17, 2012.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
