Bridge Capture™ applications

Bridge Capture™ process is illustrated in Figure 1 and the technology is illustrated in detail in Figure 8.

Bridge Capture™ is an efficient targeted pre-sequencing technology which offers a rapid, highly sensitive, platform agnostic and cost-effective molecular quantification solution.

In Bridge Capture™ the sample is targeted with Bridge Capture™ probes. A successful targeting of a specific sequence requires simultaneous binding of two probes, which are held together by a bridge oligo. Both probes must bind to their respective target sequences for the Bridge Capture™ to be successful. To ensure accurate identification of unique binding events, UMIs (see FAQ interlinks below) are included in the probes.

Once the probes have found their intended targets, the gap between probes is copied from the target sequence and ligated to form gap-filled circular probe construct, which can be optionally sequenced directly with a circular-based sequencer like Complete Genomic’s DNBSEQ, Element Aviti or PacBio Onso. This circular construct is linearly amplified by RCA to generate multiple copies of the circular probe, which can be optionally sequenced with long-read sequencing platforms, such as Oxford Nanopore Technologies.

After linear amplification, sequencing platform-specific adapters are introduced through a limited-cycle indexing PCR.

To ensure optimal quality and purity, the resulting libraries are purified with bead purification protocols. This step helps to remove any impurities and contaminants that may affect the accuracy of the sequencing data.

Bridge Capture™ is a patented laboratory process workflow. The bridge structure connects the two target-specific probes, enabling the capture of the target region and its subsequent linear amplification. This innovative design allows the targeted region to be copied to the probe gap. This permits capture of relatively long target regions while keeping the cost of probe synthesis down by using shorter individual oligos. Bridge is the upmost oligo in the structure in Figure 1.

Bridge Capture™ provides various advantages when compared to different liquid biopsy techniques. We therefore provide three separate answers for this question where Bridge Capture™ is compared to amplicon-based techniques (see FAQ interlinks below), hybrid capture-based techniques (see FAQ interlinks below) and molecular inversion probe-based techniques (see FAQ interlinks below).

One key benefit Bridge Capture™ has over all of these techniques is the capability to pool the samples directly after the targeting step without quantification. This approach ensures that the workload does not increase linearly with the number of samples, offering a distinct advantage in scalability (see FAQ interlinks below).

Yes.

The performance of Bridge Capture™ was compared against ArcherDX LiquidPlex and AmpliSeq for Illumina Cancer Hotspot Panel v2 with comparable results. All the compared technologies were carried out by a global 3rd party CRO highly experienced with NGS.

Quote from an expert technician in NGS preparations at the CRO: “This is by far the easiest workflow I’ve ever used.”

The Bridge Capture™ workflow is designed to be fast and efficient, taking less than 5 hours to complete with only 5 minutes of hands-on time required, compared to 7 hours on amplicon-based workflows or at least 8 hours on hybrid capture-based workflows. This streamlined workflow allows for rapid sample processing, saving valuable time and resources (<See Figure 1>).

Once the workflow is complete, the subsequent NGS analysis duration depends on the sequencing technology used.

Figure 1 Duration breakdown of Bridge Capture™ Tx and MRD laboratory workflows.

Yes.

Bridge Capture™ has been demonstrated to reliably detect SNVs, indels, and gene fusions. We also have preliminary results of detecting CNVs. Bridge Capture® can detect mutations associated with any cancer type, given the right panel design.

Nicking Loop™ has been demonstrated with SNVs and due to the shared functions with Bridge Capture™ we assume Nicking Loop™ to handle the same mutation types.

Yes.

The smallest amount of patient cfDNA tested with Bridge Capture™ thus far has been approximately 2000 genomic copies (5 ng). The detection of low allelic fractions benefits from a larger amount of sample used in the workflow.

The main factors that impact the sensitivity of the Bridge Capture™ are sample quality and total amount of DNA present. It is worth noting that the sensitivity varies slightly between different probes, which is most likely due to the unique binding characteristics determined by the probe and target sequences. In our publication (Adamusová et al. 2024), we observed a sensitivity range of 0.03% to 0.2% MAF, which depends on the specific probe. These MAFs were determined through serial dilutions of fragmented tumor biopsy DNA to fragmented gDNA, which were subsequently sequenced on the NovaSeq 6000. We can optimize the performance characteristics of any probes based on customer preferences.