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We recently had the pleasure of speaking to Alex Gough and Jeremy Preston, CEO/Co-Founder and CCO of Sequins, respectively. Sequins is commercializing a novel spike-in control technology developed for NGS applications to ensure standardization and more precise sequencing with initial product launches in metagenomics, WGS, and ctDNA.

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What inspired the creation of Sequins? What are the major unmet needs in genomic standards?

Sequins technology was developed in the lab of Prof. Tim Mercer at The Garvan Institute in Sydney, one of Australia’s leading genomics research institutes, to solve the team’s own challenges in NGS assay development. The program grew to an impressive footprint - like a startup within a lab, sending RUO Sequins to hundreds of external partner labs, such was the demand for a control system in NGS. A pile of publications followed, and Tim became engaged with regulatory and standards organizations to help chart the course for the next generation of genomics standards, including the FDA’s Sequencing Quality Control group.

Alex Gough, a biotech investor and entrepreneur with a background in financing and developing tools and diagnostics companies in the space, including Nuclera, Inivata, and ONT, became interested in Sequins. Realizing that there was not a standardized measurement system in NGS, yet seeing the volume and magnitude of studies, the need for inline control systems became obvious. Having seen the challenge and cost of developing complex NGS assays including MRD liquid biopsy tests, and the difficulty of comparing between sequencing technologies, Alex was quickly convinced that the ‘represent anything’ spike-ins could be an elegant universal solution, exclusively licensing the technology into the startup Sequins, and securing venture backing from US, European and Australian venture investors.

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When and why are sequencing standards typically used? What would you consider their fundamental requirements?

Most controls currently used are process controls added to the sequencing workflow as separate samples. These provide information on the workflow and assay, but do not tell you anything about the quality of each sample being sequenced. Further, any cell line control accumulates mutations over the course of passaging, resulting in drift from the documented control.

Sequins are patented synthetic nucleic acid spike-in controls that directly mirror naturally occurring sequences and act as both process and internal controls. Because Sequins retain the same nucleotide composition as the natural sequence, they enable accurate representation of genomic complexity without compromising the integrity of the sample and results. Sequins perform equivalently throughout sequencing workflows, providing a true measure of control and enabling representation of almost any genomic feature, in any organism with a reference genome. Due to our design and manufacturing flexibility, we can offer a huge variety of complexity in a single control, often genetic features that would only be found across a range of samples or controls. In addition to covering challenging regions, we can also add molecular ladders for quantitative purposes, so our controls offer multifaceted benefits to the user.

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How do the needs for standards / controls differ by type of assay (e.g., tissue vs. blood) and application (e.g., genomic profiling vs. MRD / monitoring)

The need for standardization in sequencing is growing, and we believe that clinically focused areas will drive the most demand for Sequins. Large-scale WGS programs associated with health systems will need controls for workflow monitoring and improved variant calling accuracy, as well as standardization for interoperability.

As liquid biopsies gain momentum in cancer testing, especially high-volume applications like MRD, the need to enhance the calling for low-frequency variants will be paramount as cancer patients are monitored for recurrence. To that end, we believe our controls—which represent both the variants being targeted and built-in molecular ladders to enable limit-of-detection calibration—will provide a powerful baseline and source of truth.

To address these needs, we recently launched our WGS Core Control set, which contains a range of different variant classes, including difficult genetic variants, germline variants at simple repeats, homopolymers, structural variants, common variants, microsatellites, and the mitochondrial genome. Sequins can measure the performance of a given WGS assay, enabling rapid troubleshooting and operational quality control. They also act as common reference points for standardization between samples, operators, and locations. We will soon be offering a WGS Clinical set based on the full ACMG 81 secondary findings list, that can be added to the core set.

We have also made available our ctDNA Evaluation Set, to use as a proof of concept for further customization in cancer liquid biopsy applications, with the inclusion of a molecular ladder for LOD calibration. And on the microbial front, we have launched our Metagenomics WGS Core Control Set, targeting over 50 microbial species to emulate a complex sample, also with a molecular ladder for normalization and quantification. This enables accurate analysis of microbial populations for pathogen detection, monitoring, and screening of antimicrobial-resistant bacteria.

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What are your perspectives on the emergence of newer sequencing players challenging the incumbents, and what competitive dynamics will be most impactful in the coming years?

It’s been interesting watching the proliferation of new sequencing technologies, and the increased competition is driving the cost of sequencing down after a period of some price stagnation. The upside is to the user, who can run more samples and tackle bigger science. However, the challenge of having an industry built on data production and no standardized control and measurement system will become even more of a problem. Given our unique design flexibility, Sequins can be used with any sequencing technology, and we have the potential to plug into the broad range of applications that NGS serves. We can tailor our designs to suit particular methods and applications.

We’ve successfully tested Sequins on both short-read (Illumina) and long-read (ONT) technologies and use both of these platforms to validate performance of some of our products. We can design long Sequins molecules (8-10kb), however, there are diminishing benefits in pushing this too far in terms of cost and value, so the need for reads greater than several kilobases is generally unnecessary.

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How will the emergence of these vendors impact the need for standardization in bioinformatics and data analysis?

The beauty of Sequins is that they are truly foreign to the sample but preserve the sequence context of target regions perfectly. And as stated above, they can be added to the sample but do not interfere with it or compromise the analysis. To enable analysis, we provide a decoy chromosome, which is essentially the reference alignment file for the Sequins. Analysis is generally plug and play, leveraging established alignment tools and variant calling software. Tying this back to our mirroring technology, the reads attributed to Sequins will not map to the target regions – they will only align to their decoy reference sequences.

As we become more established, we anticipate the need for more developed and refined software tools and are already planning and scaling towards this with the onboarding of key talent in the area and a longer-term goal to provide a user-interface environment where advanced analysis tools can be accessed.

Who are your target customers, and how do you expect this to evolve?

The sequencing ecosystem is huge and covers such a wide range of applications and customer types. Given that we plug into all NGS, we can serve any application that NGS serves. There are differing needs for controls depending on application. Researchers typically want the ability to standardize and enable high-value collaborative studies that can run over substantial periods, whereas clinical labs need accuracy and confidence in variant calls given they’re delivering test results to patients and want to minimize sample re-runs.  As sequencing becomes widespread in oncology testing and we see proliferation of samples and applications such as MRD offered across a multitude of locations, the need to also standardize between sites and operators will become paramount – on top of the need for accuracy and reliability.

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Can you describe your business model and longer-term plans?

Initially, we’ve gone to market with off-the-shelf sets of Sequins controls targeting certain application areas. It’s hard to serve the broader market with one-size-fits-all, and similar to what we’ve seen in the targeted sequencing space, we expect to have a lot of demand for custom control sets. Consequently, we’re most excited about our On-Demand product category, and as we become more established with a large repository of designs and synthesized Sequins molecules, we’ll be able to offer On-Demand through a simple user interface on our website. If particular Sequins molecules have already been designed and synthesized, we can readily pick and blend them. If there are novel molecules to design, we can synthesize and blend with these to create individualized sets. Our business model will therefore leverage economies of scale, where each new molecule synthesized and stored provides inventory for use over time. This model provides a huge benefit to customers as they can version their assays and controls with continuity and do so quickly.

Our vision and the future we see is informed assay design with a “controls first” approach whereby the baseline source of truth is first established, and the test is the wrapper associated with it. We believe that the missing piece of the puzzle for widespread implementation of sequencing in healthcare is the need for a standardized measuring system and the interoperability that will come from that. Most other barriers have now been solved, for example, the cost of sequencing, library prep, and analysis have come down dramatically, and there are great automation solutions.

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Thank you both for your time today!

Thank you for the opportunity to discuss our work in genomic controls and standardization. We're excited about this technology's potential impact on genomics and look forward to its continued development and application.

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