Abstract
Illumina is the leading sequencing platform in the next-generation sequencing (NGS) market globally. In recent years, MGI Tech has presented a series of new sequencers, including DNBSEQ-T7, MGISEQ-2000 and MGISEQ-200. As a complex application of NGS, cancer-detecting panels pose increasing demands for the high accuracy and sensitivity of sequencing and data analysis. In this study, we used the same capture DNA libraries constructed based on the Illumina protocol to evaluate the performance of the Illumina Nextseq500 and MGISEQ-2000 sequencing platforms. We found that the two platforms had high consistency in the results of hotspot mutation analysis; more importantly, we found that there was a significant loss of fragments in the 101–133 bp size range on the MGISEQ-2000 sequencing platform for Illumina libraries, but not for the capture DNA libraries prepared based on the MGISEQ protocol. This phenomenon may indicate fragment selection or low fragment ligation efficiency during the DNA circularization step, which is a unique step of the MGISEQ-2000 sequence platform. In conclusion, these different sequencing libraries and corresponding sequencing platforms are compatible with each other, but protocol and platform selection need to be carefully evaluated in combination with research purpose.
Highlights
With the launch of the Human Genome Project, next-generation sequencing (NGS) technology has had a huge impact on the biological field in the past 20 years (Consortium, 2015; Yang et al, 2015; Goodwin et al, 2016)
We compared the Q20 rate, GC content, mean depth and capture efficiency of 204 samples generated based on the Illumina library protocol, which were captured by the IDT 38-hotspot gene panel and sequenced on the Illumina and MGISEQ-2000 sequencing platforms (Figure 1, details in Supplementary Table S3), respectively
We found that all of the quality control parameters had significant differences, with p-values of 4.87e85, 1.15e-4, 0.0326 and 0.0035, respectively, in the two-tailed heteroscedasticity t-test analysis. We thought that these differences could be due to the sequencing principles, the algorithm used for base recognition or the sequencing platform characteristics
Summary
With the launch of the Human Genome Project, next-generation sequencing (NGS) technology has had a huge impact on the biological field in the past 20 years (Consortium, 2015; Yang et al, 2015; Goodwin et al, 2016). The Cancer Genome Atlas (TCGA) (Weinstein et al, 2013) and International Cancer Genome Consortium (ICGC) (Hudson et al, 2010) have sequenced thousands of tumors from more than 50 cancer types and summarized the significant genetic somatic mutations that occur during the process of tumorigenesis (Alexandrov et al, 2013) These data have played an extremely important role in promoting cancer genome research and development (He et al, 2020a; He et al, 2020b; Liu et al, 2021). MGI Tech Co., Ltd (referred to MGI) launched a series of NGS sequencers and platforms based on DNA nanoball (DNB) and probe-anchor synthesis (cPAS) technology, such as MGISEQ-200, MGISEQ-2000, and DNBSEQ-T7 (Fehlmann et al, 2016) They have gradually achieved a certain sales volume and have become another option for high-throughput sequencing. The selection of sequencers and platforms is becoming increasingly diversified and all theoretically compatible and applicable to each other, the choice of platform for practical applications may need to be further evaluated according to the research purpose and library characteristics
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