CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing

Genome Biol. 2018 Nov 26;19(1):202. doi: 10.1186/s13059-018-1578-y.


High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that lead to false discoveries and low sensitivity. We describe CODEX2, as a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples. We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent. CODEX2 outperforms existing methods and, in particular, significantly improves sensitivity for common CNVs.

Keywords: Copy number variation; Latent factor; Negative control; Next-generation sequencing; Normalization.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Copy Number Variations*
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Melanoma / genetics