title: Copy-number-aware differential analysis of quantitative DNA sequencing data.
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.
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland. mark.robinson@imls.uzh.ch
authors.forename: Mark D
authors.initials: MD
authors.lastname: Robinson
authors.forename: Dario
authors.initials: D
authors.lastname: Strbenac
authors.forename: Clare
authors.initials: C
authors.lastname: Stirzaker
authors.forename: Aaron L
authors.initials: AL
authors.lastname: Statham
authors.forename: Jenny
authors.initials: J
authors.lastname: Song
authors.forename: Terence P
authors.initials: TP
authors.lastname: Speed
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Clark
mesh_terms: D000465:Algorithms; D004247:DNA / Q000235:genetics; D056915:DNA Copy Number Variations; D019175:DNA Methylation; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA