美国威尔康奈尔医学中心Christopher E. Mason等研究人员合作完成DNA测序平台二代测序的性能评估。2021年9月9日出版的《自然—生物技术》杂志发表了这项成果。

生物分子资源设施协会（ABRF）二代测序研究对一组测序仪器（HiSeq/NovaSeq/paired-end 2×250-bp化学、Ion S5/Proton、PacBio循环共识测序（CCS）、牛津纳米孔技术公司PromethION/MinION、BGISEQ-500/MGISEQ-2000和GS111）在人类和细菌参考DNA样本上的表现进行了基准测试。在短读仪器中，HiSeq 4000和X10提供了最稳定、最高的基因组覆盖率，而BGI/MGISEQ的测序错误率最低。长读仪器PacBio CCS具有最高的基于参考的测绘率和最低的非测绘率。

两种长读平台PacBio CCS和PromethION/MinION在重复丰富的区域和跨同源物中显示了最好的序列映射。NovaSeq 6000使用2×250bp读数的化学方法是捕获已知插入/删除事件的最稳健的仪器。这项研究是当前基因组学技术的一个基准，也是为实验设计和下一代测序变体识别提供信息的资源。

据悉，评估大规模平行DNA测序平台的可重复性、准确性和实用性仍然是一个持续的挑战。

附：英文原文

Title: Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Author: Foox, Jonathan, Tighe, Scott W., Nicolet, Charles M., Zook, Justin M., Byrska-Bishop, Marta, Clarke, Wayne E., Khayat, Michael M., Mahmoud, Medhat, Laaguiby, Phoebe K., Herbert, Zachary T., Warner, Derek, Grills, George S., Jen, Jin, Levy, Shawn, Xiang, Jenny, Alonso, Alicia, Zhao, Xia, Zhang, Wenwei, Teng, Fei, Zhao, Yonggang, Lu, Haorong, Schroth, Gary P., Narzisi, Giuseppe, Farmerie, William, Sedlazeck, Fritz J., Baldwin, Don A., Mason, Christopher E.

Issue&Volume: 2021-09-09

Abstract: Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2×250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. The long-read instrument PacBio CCS had the highest reference-based mapping rate and lowest non-mapping rate. The two long-read platforms PacBio CCS and PromethION/MinION showed the best sequence mapping in repeat-rich areas and across homopolymers. NovaSeq 6000 using 2×250-bp read chemistry was the most robust instrument for capturing known insertion/deletion events. This study serves as a benchmark for current genomics technologies, as well as a resource to inform experimental design and next-generation sequencing variant calling.

DOI: 10.1038/s41587-021-01049-5

Source: https://www.nature.com/articles/s41587-021-01049-5