Accuracy benchmark of the GeneMind GenoLab M sequencing platform for WGS and WES analysis

Abstract

Background GenoLab M is a recently developed next-generation sequencing (NGS) platform from GeneMind Biosciences. To establish the performance of GenoLab M, we present the first report to benchmark and compare the WGS and WES sequencing data of the GenoLab M sequencer to NovaSeq 6000 and NextSeq 550 platform in various types of analysis. For WGS, thirty-fold sequencing from Illumina NovaSeq platform and processed by GATK pipeline is currently considered as the golden standard. Thus this dataset is generated as a benchmark reference in this study. Results GenoLab M showed an average of 94.62% of Q20 percentage for base quality, while the NovaSeq was slightly higher at 96.97%. However, GenoLab M outperformed NovaSeq or NextSeq at a duplication rate, suggesting more usable data after deduplication. For WGS short variant calling, GenoLab M showed significant accuracy improvement over the same depth dataset from NovaSeq, and reached similar accuracy to NovaSeq 33X dataset with 22x depth. For 100X WES, the F-score and Precision in GenoLab M were higher than NovaSeq or NextSeq, especially for InDel calling. Conclusions GenoLab M is a promising NGS platform for high-performance WGS and WES applications. For WGS, 22X depth in the GenoLab M sequencing platform offers a cost-effective alternative to the current mainstream 33X depth on Illumina.

Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019

“…To the best of our knowledge, this is the first mNGS study to systematically describe clinical HAdV genotypes and perform phylogenetic characterization using the GenoLab M platform. In our previous study, GenoLab M showed comparable performance metrics to WGS and whole-exome sequencing ( Li et al, 2022 ), transcriptomics, and LncRNA ( Liu et al, 2021 ) applications when compared in parallel with the Illumina NovaSeq sequencing platform. In the present retrospective study, we compared the applicability of the GenoLab M platform with that of the NextSeq 550 platform in mNGS.…”

Assessing the impact of sequencing platforms and analytical pipelines on whole-exome sequencing

“…Recently, GeneMind Biosciences Company Limited launched a new sequencing instrument (GenoLab M ™) based on their previous work on the GenoCare™ single-molecule sequencer ( Li et al, 2022 ), a promising sequencing platform with high performance and low cost. The GenoLab M sequencer employs SBS and reversible termination approaches, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina’s sequencing instruments.…”

“…The GenoLab M now generates 300 GB of sequence data in a single run, costing 6 USD/GB ( Liu et al, 2021 ). The previous study has shown that GenoLab M can achieve results comparable to the Illumina platform in the transcriptome, but there are few relevant studies on WES ( Li et al, 2022 ). In this study, we selected two market-proven platforms with high market share and one newly launched sequencing platform to study the impact of different sequencing platforms on WES results.…”

Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

“…In October 2020, GeneMind Biosciences Company Limited (GeneMind) launched a new sequencing instrument (GenoLab M) that is fully compatible with Illumina based libraries and does not require any library conversion [ 11 ]. It was revealed that the GenoLab M is a promising sequencing platform for transcriptomics and long non-coding RNA profiling in animal, plant, and human with comparable performance but a lower cost compared to NovaSeq 6000 (Illumina) [ 11 , 12 ]. However, the performance of the GenoLab M platform in other applications has not yet been tested, for example, for single cell sequencing including spatial transcriptomics.…”