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

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


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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • DNA / genetics
  • DNA Copy Number Variations*
  • DNA Methylation
  • Genetic Loci
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Sequence Analysis, DNA / methods*


  • DNA