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

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
    • Publication Information:
      Original Publication: London : BioMed Central, [2000-
    • Subject Terms:
    • 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.
      (© 2022. The Author(s).)
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    • Contributed Indexing:
      Keywords: GenoLab M; NA12878; Nextseq 550; NovaSeq 6000; WES; WGS
    • Publication Date:
      Date Created: 20220722 Date Completed: 20220726 Latest Revision: 20220729
    • Publication Date:
      20220908
    • Accession Number:
      PMC9308344
    • Accession Number:
      10.1186/s12864-022-08775-3
    • Accession Number:
      35869426