Aim: The aim of this study was to evaluate the suitability of the new Illumina MiSeq i100 sequencing platform for high resolution HLA typing using GenDx products.
Methods: 58 GeT-RM reference cell lines were prepared using GenDx NGSgo-MX11-3 amplification which were subsequently processed into libraries using the NGSgo® Library Full Kit. These libraries were sequenced on both the MiniSeq (high output kit) and MiSeq i100 (25M flow cell) sequencing platforms. Both the MiniSeq and MiSeq i100 runs were conducted with 2x150 reads, and an additional 2x300 read run was performed on the MiSeq i100. Multiple runs were carried out on the MiSeq i100 to show the expected variability between runs.
Results: Read quality from the MiSeq i100 was significantly improved compared to the MiniSeq in terms of %Q30 and error rate. Additionally, the sequencing run times generated on the MiSeq i100 were significantly faster with approximately 7 hr for 2x150 cycle kits compared to 24 hr on the MiniSeq. Overall, HLA typing results from the MiSeq i100 repeated runs showed high concordance as compared to the MiniSeq platform.
Conclusion: The new MiSeq i100 offers HLA typing results that were comparable to previous sequencing platforms such as the MiniSeq. The MiSeq i100 features faster run times, reduced overall costs, and a higher percentage of bases above Q30 making the MiSeq i100 platform well-suited for high-resolution HLA typing.
