cell-free (cfDNA) NGS library prep

The PrenaSeq NGS library prep kit is highly regarded for cfDNA genomics applications due to several key advantages:  

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Increased Conversion Efficiency:

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The kit is designed to maximize the conversion of fragmented cfDNA into sequenceable library molecules. This is crucial for low-input liquid biopsy samples, where the amount of cfDNA can be very limited. Higher conversion rates lead to improved library complexity and deeper sequencing coverage.  

Improved Yields from Low Input: Studies have shown that the Watchmaker kit can provide significantly higher library yields from small amounts of cfDNA (e.g., 1 ng) compared to other commercially available kits. High Coverage of Rare Variants: The increased library complexity and deeper coverage enable more sensitive and reliable detection of low-frequency variants, which is essential for applications like somatic mutation calling in cancer liquid biopsies. In some cases, it has shown a 3.5-fold improvement in coverage of rare variants compared to other kits.  

Minimized Bias and Artifacts:

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Reduced PCR Bias: The kit, especially when used with the Equinox Library Amplification Kits, is designed for high-fidelity and low-bias amplification, ensuring a more accurate representation of the original cfDNA population.  

Low Artifact Formation: The streamlined workflow helps minimize the introduction of artifacts and biases during library preparation, which is critical for accurate variant calling and avoiding false positives. This includes a reduction in false chimeric reads and hairpin artifacts, which can be problematic in other methods.  

Minimized Adapter-Dimer Contamination: The kit effectively minimizes the formation of adapter dimers, which can consume sequencing resources without providing useful information.  

Streamlined and Automation-Friendly Workflow: Fast and Simple Protocol: The library preparation can be completed in as little as two hours with a user-friendly workflow.

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Automation Compatibility:

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The kit is designed with automation in mind, including generous reagent overages and optimized protocols for liquid handling systems, such as the Hamilton Star, EP Motion NGS, Revvity Sciclone G3 NGSx workstation. This reduces hands-on time, minimizes errors, and increases throughput, which is vital for processing clinical samples.

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Compatibility with Challenging Samples:

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Effective for cfDNA and ctDNA: The kit is specifically optimized for cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) analysis, which are the primary analytes of interest in liquid biopsies.

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In summary, the PrenaSeq NGS library prep kit excels in cfDNA and liquid biopsy applications due to its ability to maximize library complexity and yield from limited input material, minimize biases and artifacts, offer a rapid and automatable workflow, and provide robust performance with challenging sample types. These features collectively contribute to higher sensitivity, accuracy, and efficiency in downstream sequencing and variant detection, which are paramount for clinical and research applications of cfDNA.