Abstract 327: A comparison of Illumina and Element Biosciences sequencing platforms
Authors: Sarah Johnson, Kevin Lee, Nathan Riccitelli
Journal: Cancer Research (2024)

Abstract Introduction: Advancements in sequencing technologies have revolutionized the field of genomics, enabling scientists to study the genetic information of organisms at unprecedented scale and speed. Next Generation Sequencing (NGS) has been utilized in clinical oncology from discovering and characterizing oncogenic driver mutations to providing personalized treatment of cancer. Among sequencing technologies, Illumina has emerged as the market leader, however, in recent years several alternatives have emerged. Herein, we evaluate the performance of NextSeq2000 and NextSeq550Dx platforms by Illumina to the Aviti platform from Element Biosciences. Method: Eight (8) Archer Core Myeloid Panel libraries previously sequenced on NextSeq550Dx as part of a validated workflow were selected, normalized to 100 nanomolar (nM), pooled and sequenced on NextSeq2000 and Aviti sequencers with 2 × 150 paired-end sequencing. Samples included the HD829 myeloid DNA control from Horizon Discovery, a well-characterized HAPMAP sample, and a mixture of HD829 in HAPMAP. Prior to sequencing on the Aviti system, libraries were circularized with the Elements Adept chemistry. Fastq files from both Aviti and NextSeq2000 sequencing were uploaded to Archer Analysis Software, standardized filtering was applied to all generated datasets, and results compared across platforms. Result: Aviti and NextSeq2000 platforms exhibited comparable sequencing reads, with an average total reads per sample of 76,205,719 and 74,201,570 from Aviti and NextSeq2000, respectively, while the lower throughput NextSeq550 platform yielded an average 17,619,350 reads per sample. Standardized filtering across all platforms provided 100% detection of true positives, however additional false positives (FP) were present in all samples and platforms that mapped to regions requiring normal dataset correction as part of the validated NextSeq550 workflow. The lowest numbers of FPs were detected on the Aviti platform, while both NextSeq550 and NextSeq2000 derived results contained several FP calls at elevated (&amp;gt;10%) variant allele frequency (VAF). Conclusion: The three platforms compared in this study were able to detect all true positives of the tested samples using the same filtering criteria. The performance metrics of NextSeq2000 and Aviti were comparable and higher than NextSeq550Dx, in line with expectations due to the higher sequencing capacity. Although the Aviti platform required additional hands-on time, it in-turn generated cleaner data with less FP variants in comparison to Illumina’s sequencing platforms. Overall, these results indicate robust sequencing throughout all three platforms. Citation Format: Sarah Johnson, Kevin Lee, Nathan Riccitelli. A comparison of Illumina and Element Biosciences sequencing platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 327.