Genomics Inform.  2019 Sep;17(3):e32. 10.5808/GI.2019.17.3.e32.

Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

  • 1Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
  • 2Department of Bioscience, University of Science and Technology, Daejeon 34113, Korea.
  • 3Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
  • 4Department of Surgery, University of Ulsan College of Medicine, Seoul, Korea.
  • 5Department of Cancer Research, Institute of Innovative Cancer Research and Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.


Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.


benchmarking; HiSeq 4000; MGISEQ-2000

MeSH Terms

Colonic Neoplasms
Quality Control
Sequence Analysis, RNA*
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