Genomics

Avidite Base Chemistry (ABC)

Avidite Base Chemistry (ABC) is the core sequencing technology developed by Element Biosciences for its AVITI and AVITI24 Systems. It is an innovative, next-generation sequencing (NGS) method that differs fundamentally from traditional sequencing-by-synthesis (SBS) by separating the enzymatic steps of sequencing. ABC utilizes a combination of proprietary advancements, including rolling circle amplification (RCA) and avidite molecules, to achieve high accuracy, lower costs, and increased flexibility.

How ABC works

The ABC workflow involves three main stages that are optimized independently:

• PCR-free amplification: Unlike other NGS platforms that use PCR-based bridge amplification, ABC uses rolling circle amplification (RCA). A circularized DNA library is used as a template to generate a continuous strand of DNA that forms a “polony”—a cluster of identical library copies.
• Separate sequencing steps: Traditional SBS combines base detection and strand extension into a single enzymatic step, which requires high concentrations of reagents. ABC separates these steps to optimize conditions for each.
• Avidite-based detection: Instead of using nucleotides with a reversible terminator and cleavable fluorophore, ABC uses fluorescently labeled “avidites”. These are polymers carrying many identical nucleotides that bind to multiple sites on the polony. Their strong, multivalent binding creates an ultrastable complex for imaging, allowing for accurate base detection with a 100-fold lower reagent concentration than SBS. After imaging, the avidites are washed away without damaging the DNA, leaving it “scarless” for the next cycle.

Key Features

• Rolling circle amplification (RCA): This PCR-free amplification method reduces common sequencing artifacts such as index hopping, optical duplicates, and errors in difficult-to-sequence regions like homopolymers.
• Low-binding surface chemistry: The flow cell is coated with a low-binding surface chemistry that minimizes non-specific binding. This increases the signal-to-noise ratio, leading to clearer images and higher accuracy, even at high polony densities.
• Two-step sequencing: By decoupling base detection from strand extension, ABC can optimize the enzyme and reagent conditions for each step individually. This increases accuracy and efficiency while significantly reducing reagent usage.
• Modular design: The underlying ABC technology is flexible and extensible. Features like the polymer core, dyes, and nucleotide linkers can be optimized for different applications, from standard DNA and RNA sequencing to multiomic workflows.
• Broad library compatibility: ABC supports a wide range of sequencing applications and is compatible with both native Element libraries and most third-party libraries.

Advantages

• High accuracyABC’s combination of RCA, optimized enzymatic steps, and multivalent avidite binding leads to superior data quality. Studies have shown higher mapping and variant calling accuracy, especially in challenging regions like homopolymers, when compared to other platforms.
• Lower sequencing costsThe high stability of the avidite complexes enables the use of nanomolar concentrations of reagents, a massive reduction compared to traditional SBS. This significantly lowers the cost per gigabase.
• Increased flexibilityThe dual, independent flow cell design of the AVITI systems, combined with ABC’s robust chemistry, allows for flexible throughput and the ability to run two different experiments simultaneously. This reduces the need for batching and improves lab efficiency.
• Reduced artifactsThe PCR-free RCA eliminates amplification bias and error propagation that can affect PCR-based methods, resulting in higher library complexity and lower duplication rates.