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

Yuchao Jiang, Rujin Wang, Eugene Urrutia, Ioannis N Anastopoulos, Katherine L Nathanson, Nancy R Zhang
2017 bioRxiv   pre-print
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, 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
more » ... trate 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.
doi:10.1101/211698 fatcat:olj26gryqfgtphwwuarh4fmwle