Characterization and mitigation of fragmentation enzyme-induced dual stranded artifacts.
Characterization and mitigation of fragmentation enzyme-induced dual stranded artifacts.
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DOI：
10.1093/nargab/lqaa070
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发表时间：
2020-12
影响因子：
4.6
通讯作者：
Blachly JS
中科院分区：
文献类型：
--
作者：
Gregory T;Ngankeu A;Orwick S;Kautto EA;Woyach JA;Byrd JC;Blachly JS
高通量短读段测序依赖于片段化的DNA以用于输入核酸的最佳采样。一些供应商现在提供专有的酶鸡尾酒作为一种更便宜，更精简的破碎方法相比，声学剪切。我们已经发现，这些酶诱导形成包含来自相反链的邻近DNA区域的文库分子。衍生自这些分子的测序读段可以导致以<5%的变体等位基因频率出现的人工产物衍生的变体调用。我们提出了片段化检测和消除（FADE），软件从映射的读数中去除这些伪影，并减轻对下游分析的伪影相关影响。我们发现伪影主要影响对测序读数中1-3%伪影偏倚敏感的下游分析，例如靶向重测序和罕见变异发现。
High-throughput short-read sequencing relies on fragmented DNA for optimal sampling of input nucleic acid. Several vendors now offer proprietary enzyme cocktails as a cheaper and more streamlined method of fragmentation when compared to acoustic shearing. We have discovered that these enzymes induce the formation of library molecules containing regions of nearby DNA from opposite strands. Sequencing reads derived from these molecules can lead to artifact-derived variant calls appearing at variant allele frequencies <5%. We present Fragmentation Artifact Detection and Elimination (FADE), software to remove these artifacts from mapped reads and mitigate artifact-related effects on downstream analysis. We find that the artifacts principally affect downstream analyses that are sensitive to a 1–3% artifact bias in the sequencing reads, such as targeted resequencing and rare variant discovery.