Copy-number-aware differential analysis of quantitative DNA sequencing data
- Mark D Robinson1,4,
- Dario Strbenac2,
- Clare Stirzaker2,
- Aaron L Statham2,
- Jenny Z Song2,
- Terence P Speed3 and
- Susan J Clark2
- 1 University of Zurich;
- 2 Garvan Institute of Medical Research;
- 3 Walter and Eliza Hall Institute of Medical Research
- ↵* Corresponding author; email: mark.robinson{at}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.
- Received February 13, 2012.
- Accepted August 7, 2012.
- © 2012, Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
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