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新型 MGISEQ-2000 测序平台与 Illumina HiSeq 2500 全基因组测序的比较分析。

Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing.

机构信息

Pirogov Russian National Research Medical University, Moscow, Russia.

Zenome.io, Ltd., Moscow, Russia.

出版信息

PLoS One. 2020 Mar 16;15(3):e0230301. doi: 10.1371/journal.pone.0230301. eCollection 2020.

DOI:10.1371/journal.pone.0230301
PMID:32176719
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7075590/
Abstract

The MGISEQ-2000 developed by MGI Tech Co. Ltd. (a subsidiary of the BGI Group) is a new competitor of such next-generation sequencing platforms as NovaSeq and HiSeq (Illumina). Its sequencing principle is based on the DNB and the cPAS technologies, which were also used in the previous version of the BGISEQ-500 device. However, the reagents for MGISEQ-2000 have been refined and the platform utilizes updated software. The cPAS method is an advanced technology based on the cPAL previously created by Complete Genomics. In this paper, the authors compare the results of the whole-genome sequencing of a DNA sample from a Russian female donor performed on MGISEQ-2000 and Illumina HiSeq 2500 (both PE150). Two platforms were compared in terms of sequencing quality, number of errors and performance. Additionally, we performed variant calling using four different software packages: Samtools mpileaup, Strelka2, Sentieon, and GATK. The accuracy of SNP detection was similar in the data generated by MGISEQ-2000 and HiSeq 2500, which was used as a reference. At the same time, a separate indel analysis of the overall error rate revealed similar FPR values and lower sensitivity. It may be concluded with confidence that the data generated by the analyzed sequencing systems is characterized by comparable magnitudes of error and that MGISEQ-2000 and HiSeq 2500 can be used interchangeably for similar tasks like whole genome sequencing.

摘要

MGISEQ-2000 由 MGI 科技有限公司（华大基因集团的子公司）开发，是 NovaSeq 和 HiSeq（Illumina）等下一代测序平台的新竞争对手。其测序原理基于 DNB 和 cPAS 技术，这些技术也应用于上一代 BGISEQ-500 设备中。然而，MGISEQ-2000 的试剂经过了改进，平台利用了更新的软件。cPAS 方法是一种基于先前由 Complete Genomics 创建的 cPAL 的先进技术。在本文中，作者比较了在 MGISEQ-2000 和 Illumina HiSeq 2500（均为 PE150）上对俄罗斯女性供体 DNA 样本进行全基因组测序的结果。从测序质量、错误数量和性能等方面对两个平台进行了比较。此外，我们使用了四个不同的软件包进行变体调用：Samtools mpileaup、Strelka2、Sentieon 和 GATK。在使用 HiSeq 2500 作为参考的情况下，MGISEQ-2000 生成的数据的 SNP 检测准确性与 HiSeq 2500 相似。同时，对整体错误率的单独插入缺失分析显示出相似的 FPR 值和较低的灵敏度。可以有把握地得出结论，分析的测序系统生成的数据具有可比的错误幅度，并且 MGISEQ-2000 和 HiSeq 2500 可以在类似的任务（如全基因组测序）中互换使用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/b660e7343239/pone.0230301.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/2af89593fb2d/pone.0230301.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/39a0c920ed45/pone.0230301.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/4766c9557793/pone.0230301.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/b660e7343239/pone.0230301.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/2af89593fb2d/pone.0230301.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/39a0c920ed45/pone.0230301.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/4766c9557793/pone.0230301.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a9bf/7075590/b660e7343239/pone.0230301.g004.jpg

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