Liquid Biopsies and Avida Technology: Advancing Cancer Detection

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Liquid biopsies offer a non-invasive way to detect various cancers through blood tests, often by capturing cell-free DNA (cfDNA) using oligonucleotide probes. Shorter probes can accelerate the analysis process, but they can also compromise specificity.

“Short probes have less sequence complexity, which can lead to reduced specificity,” explains Michael Ruvolo, a genomics R&D scientist at Agilent Technologies. To address this challenge, Agilent developed its Avida* NGS target enrichment technology, which uses a synergistic probe binding system. This approach combines short probes with longer ‘anchor’ sequences to create a 3D binding structure that effectively captures the desired DNA. “This design drastically reduces the chances of binding to off-target sequences,” says Ruvolo, “delivering both high specificity and the rapid turnaround enabled by shorter probes.”

Precision Targeting in Liquid Biopsies

In a recent application note, Ruvolo explored how Avida performs in various scenarios for detecting specific DNA sequences and methylation patterns. One key focus was the technology’s ability to consistently identify unique molecules at varying sample input levels.

By calculating the theoretical number of target molecules based on genome weight and sample input, Ruvolo found that Avida recovered approximately 72–75% of these molecules. “That’s at least twice the recovery rate of many other systems we’ve tested,” he notes.

This high sensitivity is particularly valuable for liquid biopsy samples, where tumor DNA can be extremely limited. “Even if tumor DNA makes up just 0.5% or 0.2% of the total DNA, the system can detect it because it captures such a high proportion of molecules,” he adds.

Ruvolo also evaluated three different Avida cancer panels. The Focused and Expanded panels are designed for deep sequencing and detection of low-frequency variants. The Discovery panel, which covers over 600 genes, supports broad genomic profiling. On-target specificity for these panels ranged from 70% to 88%, with lower values associated with regions used for translocation detection, which are often less unique and thus more challenging to target precisely.

Detecting DNA and Methylation Together

Beyond DNA targets, the Avida platform also supports methylation analysis, available either as a standalone kit or in a combined ‘Duo’ kit. The Duo kit enables researchers to detect both mutation and methylation markers from a single sample.

“The Duo workflow is ideal for researchers seeking high sensitivity for both mutation and methylation detection with minimal sample input,” says Ruvolo. He emphasizes that the Duo kit performs just as well as the individual DNA or Methylation kits. “Both methods achieve strong enrichment and deliver equivalent results functionally,” he says. According to the application note, both systems achieved close to 90% on-target reads.

Streamlined Workflow for Broader Access

Along with its high sensitivity and specificity, the Avida system is also designed for ease of use. “Unlike traditional methods, Avida eliminates a sample amplification step, simplifying and shortening the workflow,” says Ruvolo. “This streamlined process makes it easier for labs to adopt and implement the technology.”