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Genome Res. 2012 Dec;22(12):2489-96. doi: 10.1101/gr.139055.112. Epub 2012 Aug 9.

Copy-number-aware differential analysis of quantitative DNA sequencing data.

Author information

1
Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland. mark.robinson@imls.uzh.ch

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.

PMID:
22879430
PMCID:
PMC3514678
DOI:
10.1101/gr.139055.112
[Indexed for MEDLINE]
Free PMC Article

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