Lang Jidong, Sun Jiguo, Yang Zhi, He Lei, He Yu, Chen Yanmei, Huang Lei, Li Ping, Li Jialin, Qin Liu
Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China.
NAR Genom Bioinform. 2022 Apr 21;4(2):lqac033. doi: 10.1093/nargab/lqac033. eCollection 2022 Jun.
Nanopore sequencing, also known as single-molecule real-time sequencing, is a third/fourth generation sequencing technology that enables deciphering single DNA/RNA molecules without the polymerase chain reaction. Although nanopore sequencing has made significant progress in scientific research and clinical practice, its application has been limited compared with next-generation sequencing (NGS) due to specific design principle and data characteristics, especially in hotspot mutation detection. Therefore, we developed Nano2NGS-Muta as a data analysis framework for hotspot mutation detection based on long reads from nanopore sequencing. Nano2NGS-Muta is characterized by applying nanopore sequencing data to NGS-liked data analysis pipelines. Long reads can be converted into short reads and then processed through existing NGS analysis pipelines in combination with statistical methods for hotspot mutation detection. Nano2NGS-Muta not only effectively avoids false positive/negative results caused by non-random errors and unexpected insertions-deletions (indels) of nanopore sequencing data, improves the detection accuracy of hotspot mutations compared to conventional nanopore sequencing data analysis algorithms but also breaks the barriers of data analysis methods between short-read sequencing and long-read sequencing. We hope Nano2NGS-Muta can serves as a reference method for nanopore sequencing data and promotes higher application scope of nanopore sequencing technology in scientific research and clinical practice.
纳米孔测序，也称为单分子实时测序，是一种第三代/第四代测序技术，能够在无需聚合酶链反应的情况下解析单个DNA/RNA分子。尽管纳米孔测序在科学研究和临床实践中取得了重大进展，但由于其特定的设计原理和数据特征，与下一代测序（NGS）相比，其应用受到限制，尤其是在热点突变检测方面。因此，我们开发了Nano2NGS-Muta作为基于纳米孔测序长读长进行热点突变检测的数据分析框架。Nano2NGS-Muta的特点是将纳米孔测序数据应用于类似NGS的数据分析流程。长读长可以转换为短读长，然后结合用于热点突变检测的统计方法，通过现有的NGS分析流程进行处理。Nano2NGS-Muta不仅有效避免了纳米孔测序数据的非随机误差和意外插入缺失（indel）导致的假阳性/阴性结果，与传统的纳米孔测序数据分析算法相比提高了热点突变的检测准确性，而且打破了短读长测序和长读长测序之间数据分析方法的壁垒。我们希望Nano2NGS-Muta能够作为纳米孔测序数据的参考方法，并促进纳米孔测序技术在科学研究和临床实践中的更高应用范围。
