Deconvolution of Complex DNA Repair (DECODR): Establishing a Novel Deconvolution Algorithm for Comprehensive Analysis of CRISPR-Edited Sanger Sequencing Data.
Deconvolution of Complex DNA Repair (DECODR): Establishing a Novel Deconvolution Algorithm for Comprehensive Analysis of CRISPR-Edited Sanger Sequencing Data.
复制标题
DOI：
10.1089/crispr.2020.0022
复制
发表时间：
2021-03
期刊：
影响因子：
--
通讯作者：
Kmiec EB
中科院分区：
文献类型：
--
作者：
Bloh K;Kanchana R;Bialk P;Banas K;Zhang Z;Yoo BC;Kmiec EB
在CRISPR指导的基因编辑过程中，多种基因修复机制相互作用，在编辑的细胞群体中产生广泛且在很大程度上不可预测的序列变化。先前可用的基于提议的插入和缺失（indel）分析软件固有的缺点使得有必要开发更全面的工具，该工具可以检测更大范围和种类的indel，同时保持当前可用工具的易用性。为此，我们开发了复杂DNA修复的去卷积（DECODR）。DECODR可以检测由单指导或多指导CRISPR实验形成的indel，而对indel大小没有限制。该软件在确定克隆扩增和批量细胞群体DNA提取物中插入和缺失碱基的身份和位置方面是准确的。任何潜在插入缺失的准确鉴定和输出允许在潜在地利用供体DNA序列、CRISPR-Cas和内源DNA修复途径的任何配置的实验中执行DECODR分析。
During CRISPR-directed gene editing, multiple gene repair mechanisms interact to produce a wide and largely unpredictable variety of sequence changes across an edited population of cells. Shortcomings inherent to previously available proposal-based insertion and deletion (indel) analysis software necessitated the development of a more comprehensive tool that could detect a larger range and variety of indels while maintaining the ease of use of tools currently available. To that end, we developed Deconvolution of Complex DNA Repair (DECODR). DECODR can detect indels formed from single or multi-guide CRISPR experiments without a limit on indel size. The software is accurate in determining the identities and positions of inserted and deleted bases in DNA extracts from both clonally expanded and bulk cell populations. The accurate identification and output of any potential indel allows for DECODR analysis to be executed in experiments utilizing potentially any configuration of donor DNA sequences, CRISPR-Cas, and endogenous DNA repair pathways.