Comparison Of Illumina Novaseq 6000 And Mgiseq-2000 In Profiling Xenograft Models.

Abstract BACKGROUND: Comprehensive genomic profiling of tumor models, including patient-derived xenografts, cell lines and organoids, is an integral prerequisite for productive in vivo studies. There are now two leading sequencing platforms from Illumina and MGI Tech. In this study, we compared the performance of the two platforms in sequencing xenograft tumors, which contain both human tumor cells and mouse stromal cells. METHODS: We performed genomic profiling on several xenograft tumors by both sequencers, including RNA-seq and whole-exome sequencing (WES) for 3 samples, and whole-genome sequencing (WGS) for 1 sample. We then performed a comprehensive assessment of sequencer performance using multiple criteria. RESULTS: The mouse ratios from the two sequencers were very close in all RNA-seq/WES/WGS datasets, indicating no or similar species bias for both platforms. The RNA-seq datasets showed high gene expression concordance, with Pearson correlation coefficients of 0.993, 0.992 and 0.993. The WES datasets showed high mutation concordance, with the mutation overlapping rates of 98.9%, 99.3% and 99.1%, and the mutation ratio correlation coefficients of 0.971, 0.976 and 0.977. The WGS data showed overall overlapping rate of 95.5%, and mutation ratio correlation coefficient of 0.955, while for SNPs and INDELs, the overlapping rate was 97.1% and 86.1%. CONCLUSIONS: Our study shows that the MGISEQ and Illumina sequencers have comparable performance in sequencing xenograft tumors. Citation Format: Wubin Qian, Xiaobo Chen, Henry Q. Li, Sheng Guo. Comparison of Illumina NovaSeq 6000 and MGISEQ-2000 in profiling xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 259.