RT Journal
A1 Robinson, Mark D.
A1 Strbenac, Dario
A1 Stirzaker, Clare
A1 Statham, Aaron L.
A1 Song, Jenny
A1 Speed, Terence P.
A1 Clark, Susan J.
T1 Copy-number-aware differential analysis of quantitative DNA sequencing data
JF Genome Research 
JO Genome Research 
YR 2012 
FD December 01 
VO 22 
IS 12 
SP 2489 
OP 2496 
DO 10.1101/gr.139055.112 
UL http://genome.cshlp.org/content/22/12/2489.abstract 
AB 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.