During this year’s American Society of Human Genetics (ASHG) meeting in Boston, MA, GEN sat down with Steve Barnard, PhD, to discuss Illumina’s progress on its multiomics strategy. Recently, the company has made major moves in the multiomics direction, including launching proteomics and single cell applications followed by a spatial technology product launched earlier this year. In his conversation with GEN, Barnard noted that the response to these rollouts from the scientific community has been positive and that customers can look forward to even more capabilities next year. The discussion also covered planned upgrades to Illumina’s sequencers as well as how the company is responding to new competition.
The interview has been edited for length and clarity.
Thomas: How has this year’s conference been so far for you?
Barnard: It has been exciting from Illumina’s point of view. We are in year two of the strategy we announced last year, with our movement towards providing the most comprehensive biological insights possible. We are expanding on the multiomics vertical and across the horizontal of the multimodal capabilities. We are doing this because it fills a deep market need that is currently missing—in providing the ability to create comprehensive biological information. We will complete that goal next year, when all the roadmap technologies will be on the market, [and we] will have a strong portfolio of products to support our customers.
Thomas: That’s a topic I was hoping we could dig into more. Illumina has purchased several companies, including single cell and proteomics technologies. At this stage, can you give me a sense of what sort of feedback you’re getting from the market? Is the community interested in getting their omics needs supported by a single company?
Barnard: When we came up with the strategy at Illumina, there’s some part of every strategy you do internally, and some part you do externally. To become a single source for the full span of omics capabilities, we needed a strong foundation for each of the technologies. We built this in part through a series of acquisitions.
Chief Technology Officer
Illumina [Illumina]
The first company we purchased was Partek, and that was the market leading biological information visualization software. It was a small company but with thousands of users, and we’ve now integrated that [software] into DRAGEN [Illumina’s flagship secondary analysis platform]. So that technology is part of the basis of our Illumina Connected Insights and Illumina Connected Multiomics software.
The second purchase we made was a company called Fluent Biosciences. That was a single cell company, [with] technology based on hydrogel beads that you encapsulate in emulsions. The importance there is the emulsion creates millions of individual reaction chambers, in which you can do biochemistry. They had single cell products on the marketplace when we purchased them. So, we’re creating that roadmap and that’s evolving. The third company that we’ve had a long relationship with over three years now is SomaLogic. It’s essentially the SomaLogic technology that we’ve purchased, and that’s expected to clear regulatory body approval early next year. That’s the proteomics technology based on aptamers and that’s the basis of the Illumina Protein Prep product.
We are now in the market development phase of those technologies. Of the three, the single cell technology was the first to be on market as Illumina Single Cell 3′ RNA Prep, and that’s gone well. We’ve announced a [single cell project] with the Broad [and] we’ll talk about that more publicly as the year goes on. But we’re happy about the data that’s being produced and the insights. The response to Illumina Protein Prep has also very [positive]. The reason for that is people are realizing that they really need the total view into the proteome. So [with that] product you can interrogate about 9,500 proteins. The circulating proteome is estimated to be around 20,000, give or take. With those projects coming to fruition, we have this beautiful portfolio of products. The response has been wonderful here at the conference and outside of the conference.
Thomas: As Illumina builds towards a one-stop-shop for all things omics, how are you thinking about approaching customers who already have their single cell and proteomics needs met by other providers? What is your sense of where those folks stand?
Barnard: While Illumina has led the industry in many ways, what you’re describing is essentially a fast follower situation. We weren’t the first to have a single cell product on the market, and we weren’t first to have a proteomics product on the market. So, 10x was certainly the first company to start developing a single cell marketplace, and Olink was probably the first antibody-based affinity technology out on the marketplace. This is just normal market conditions where you start entering fields [with] incumbent players. Before we do that, we always look at our technology roadmaps and say this has to be a factor of 2-5 better to get people to convert from what they’re used to. We’re in the market development phase where people are starting to realize the power of the Illumina Protein Prep product and the scalability of our single cell product, [which are] both complete, end-to-end solutions. So, it’ll take a little bit of time, but we’ll get there.
Thomas: We’ve talked about the different legs that make up your strategy. Are there plans to add to it?
Barnard: We will always be investing in platforms or our sequencing systems and evolving those to market conditions and what the market needs. So that’s number one and expect to see more of that. [At ASHG], I talked about upgrades for the MiSeq i100 and then the upgrades to the NovaSeq X that are coming in 2026. We’ll continue investing in that because it is extremely important.
On top of that is the multiomics and the multimodal because you can exploit the power of our installed base, the instruments, and start layering on these assays to fill in the gaps of biology. So each of those, the Illumina Protein Prep or the single cell or the 5-base genome or Constellation, has a roadmap that extends 5-10 years out and we know exactly what is needed in those areas. So we’ll keep investing in [them]. A simple example of that is Illumina Protein Prep where we’re at 9,500 proteins, which is about 50% of the proteome. We’ll continue adding to that until we get to the full proteome.
The third one is wrapping all of this with our new division called BioInsights. [Think] about the amount of data that’s going to be produced between these sequencing systems and then layering all the omics from proteomics to transcriptomics to epigenetics to genomics, and all the other omics we’re not even talking about yet. And then across the multimodal space, you are talking about the number of samples, the total number of cells or different cells, or whether it’s blood or plasma. To make sense of that data, you’re going to [need] infrastructure, bioinformatics, AI, and machine learning.
Thomas: I did want to pivot to talking about the bigger market picture which includes some new players. At this meeting, in particular, Roche has been discussing its SBX technology including presenting new data. What are your thoughts on more competitors entering the market? Are you worried at all?
Barnard: Let’s take a step back. The market is maturing and there’s so much revenue dollars that a lot of players are trying to capture. For Roche, with its diagnostic division and relationship to drug development, it makes sense for them to be interested in this market. What we’re seeing now is their technology is turning the corner. The data being produced seems real, but there’s a huge difference between the data being real, in isolated incidents, in an academic sense and being useful in the marketplace. And this is the phase they’re in, which any young early release technology goes through. So, it’s really a wait and see what the technology delivers. From Illumina’s point of view, our roadmaps are extremely strong. So, I think we have roadmaps and products that will compete in the marketplace.
Thomas: I’m assuming you’ve heard that in one of the sessions, Roche revealed the pricing for its sequencing platform [$750,000] minus the costs of consumables and things like that. Does that price point concern you?
Barnard: I’ll start by saying that the investment by companies entering sequencing speaks to the continued strength and potential of the market. We welcome competition, it makes us stronger, it’s good for science and for our customers. The reality is, the sequencer is only a piece of the puzzle, and customers have to consider the complete cost of workflow and its range of capabilities—how much can you do with that box? That’s precisely why we’re focused on delivering a robust offering of complete omic solutions that can be run on a single platform. The future is about our ability to increase diagnostic yield, which will be enabled by products that provide deeper, broader biologic insights, like our 5-base and Constellation technologies. No other company has such a powerful portfolio. I’ll add that emerging technologies take considerable time to go from development to launch to adoption. It’s still early, we’ll look forward to seeing published data to assess the accuracy, data quality, consistency, as well as end-to-end cost.
Thomas: As we wrap up, any final thoughts?
Barnard: I think it’s extremely important to point out that we’re in the middle of our multi-year strategy. Part of that strategy is executing on our roadmap and delivering our products to the market. They’re having the impacts we hoped they would, and people are proving that with the customer experiences. Next year, our whole vision of integrated multiomic and multimodal total workflows will be complete to a large degree. It really is an exciting time for Illumina to be talking about this.