CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing
CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing
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DOI：
10.1186/s13059-018-1578-y
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发表时间：
2018-11-26
期刊：
影响因子：
12.3
通讯作者：
Zhang, Nancy R.
中科院分区：
文献类型：
--
作者：
Jiang, Yuchao;Wang, Rujin;Zhang, Nancy R.
与基于阵列的方法相比，高通量DNA测序能够以更高的分辨率检测全基因组范围内的拷贝数变异（CNV），但存在导致错误发现和低灵敏度的偏差和伪影。我们将CODEX 2描述为全谱CNV分析的统计框架，该框架对常见和罕见人群频率的变异敏感，适用于有或无阴性对照样本的研究设计。我们在全外显子组和靶向测序数据上证明和评估CODEX 2，其中偏倚最突出。CODEX 2优于现有方法，特别是显着提高了常见CNV的灵敏度。
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.