Get More Out of Your Flow Cell with 3X Fold Enrichment

DNA fragmentation, a key step in next-generation sequencing (NGS) library preparation, is primarily achieved through two methods: mechanical and enzymatic shearing. Mechanical fragmentation uses physical forces (e.g., ultrasonication or nebulization) to break DNA into smaller fragments. In contrast, enzymatic shearing utilizes specific enzymes to cut DNA strands at specific points.¹

Figure 1. 3x Fold Enrichment1¹

Mechanical shearing is often preferred due to its ability to yield consistent fragment sizes and maintain DNA integrity. However, enzymatic shearing also offers benefits, such as requiring no upfront capital expenditure and can sometimes be more suitable for certain types of DNA samples.^3,4

One critical parameter in NGS is fold enrichment, particularly in hybrid capture workflows. It indicates the level of target DNA sequences that have been enriched in the library following the hybridization step. A higher fold enrichment indicates a greater prevalence of target DNA sequences, resulting in more uniform batches and a decrease in assay failure rates. A lower fold enrichment, however, can imply that a significant portion of the exome hasn’t been adequately covered. This might necessitate additional sequencing to achieve sufficient coverage across all exonic regions for accurate variant calling.

Moreover, there’s a direct correlation between upfront fragmentation and post-hybridization enrichment, which has significant implications for sequencing economics. The higher target enrichment that can be achieved with Covaris technology reduces the need for repeated sequencing to obtain the necessary coverage, saving both time and money. Additionally, the ability to accommodate more samples on a flow cell further enhances cost-effectiveness and efficiency.

Data from the analysis of 95,000 exomes, shown in Figure 1, demonstrates that Covaris technology provides a 3X higher target enrichment compared to a leading enzymatic preparation. This leads to more precise targeting, the creation of more uniform batches, as well as lower assay failure rates in whole exome sequencing (WES) or targeted panel pipelines.

These cost savings, when combined with a lower duplication rate, higher sample pass rate, and more consistent fragment size distribution, result in Covaris being not only the highest quality sample prep solution on the market, but also the most economical.

References

1. Quest Diagnostics with Covaris launches automated NGS platform, optimizing workflows to maximize lab. www.youtube.com. Accessed November 1, 2023. https://www.youtube.com/watch?v=dqWaCWVHqjI‌
2. Bitesize Bio. Shearing DNA for Next-Generation Sequencing: Which Method Should I Choose? https://bitesizebio.com/13581/shearing-dna-for-next-generation-sequencing-which-method-should-i-choose/
3. Gao, L., Liu, X., Xu, H., Lu, Y., Li, M., & Wu, J. (2022). Comparative evaluation of mechanical and enzymatic methods for DNA fragmentation in the preparation of NGS libraries. BMC Genomics, 23(1). https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08316-y
4. Genohub Blog. (2016, July 22). Fragmentation of DNA/RNA for Next Gen Sequencing Library Prep. https://blog.genohub.com/2016/07/22/fragmentation-of-dna-rna-for-next-gen-sequencing-library-prep/

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