NEW YORK – Illumina is jumping upstream in the spatial biology market with a new technology offering revealed on Wednesday. The firm also announced a collaboration with the Broad Institute to offer the technology to researchers and demonstrate its ability to produce large-scale spatial transcriptome datasets.
Unsurprisingly, the technology uses Illumina sequencing as a readout, specifically on the mid-throughput NextSeq and high-throughput NovaSeq instrument lines. The method begins by placing fresh-frozen tissue sections onto a pre-mapped and barcoded array with a capture area of approximately 15 mm by 50 mm. First, the slide undergoes H&E staining and imaging, followed by RNA capture and conversion into a sequencing library, with data analysis performed by a new software suite.
According to Illumina, the new platform offers feature resolution of 1 µm and "bins together" transcripts using an algorithm that also takes into account the H&E staining information, creating data at the single-cell level. The number of transcripts detected per cell depends on tissue type and quality, but Illumina suggested that it can detect over 1,000 transcripts per cell, with around 600 to 1,000 genes per cell.
"The combination of whole transcriptome and cellular resolution is really what I think has been missing from spatial," said Darren Segale, senior director of scientific research at Illumina. "Right now, you kind of have to choose one or the other. This product gives you the opportunity to have them both."
Researchers at the Broad Institute are already lining up to try out the Illumina technology, according to Sami Farhi, director of the Broad Spatial Technology Platform (STP), which will be conducting the assay as part of the collaboration, with sequencing performed at Broad Clinical Labs. The ability to capture poly-A RNAs, along with the high resolution and large capture area, "is unique to some degree," he said. The collaboration between the Broad and Illumina aims to "generate large-scale, coordinated data from hundreds of samples," the partners said in a statement.
The announcement is a testament to Illumina's ability to work in secret on a hot new technology. Though the company had not publicly indicated it was working on its own spatial platform, Illumina's expertise in arrays and nucleic acid chemistry meant it had everything it needed to develop one. Moreover, others were already using Illumina technology to conduct spatial biology experiments, so surely Illumina could, if it wanted to.
Over the past several years, for example, researchers have hacked late-model Illumina sequencers, turning them into tools for spatial biology. In 2021, researchers from the University of Michigan described SeqScope, a method to do spatial transcriptomics using the Illumina MiSeq. Last year, that group and another team independently showed they could increase the scale of their experiments using the NovaSeq 6000 high-throughput sequencer.
Also, in 2022, researchers from the New York Genome Center posted a preprint describing their efforts to turn an old HiSeq sequencer into a spatial proteomics instrument.
As sequencing startups Singular Genomics Systems and Element Biosciences have embraced additional modes of analysis, industry observers have pestered Illumina officials for indications that the firm's embrace of multiomics would include spatial biology as well as proteomics and single-cell sequencing.
At a launch event for Illumina's MiSeq i100 in September, CEO Jacob Thaysen declined to offer any information about whether the firm was working on a spatial platform. Now, it appears it was nearly done.
"I think it was about time," said Luciano Martelotto, a spatial biology expert at the University of Adelaide. "Illumina should be a bigger player now, with other sequencing companies doing the same."
Development took approximately two years, Illumina Chief Technology Officer Steve Barnard said, and was prioritized by Thaysen after he took the helm in late 2023. Illumina's experience in manufacturing array technology was a key enabler. "We're able to encode biological information in a random X-Y pattern and then simply and inexpensively map that," Barnard said.
Offering a look at the whole transcriptome and using sequencing as a readout, the Illumina spatial tech may be more comparable to MGI Tech's Stereo-seq and Curio Bioscience's Seeker platforms than the Element and Singular offerings — which for now comprise targeted, multiomic panels of hundreds of RNAs plus dozens of proteins. 10x Genomics' Visium line, including the new HD version, also uses sequencing as a readout and offers the ability to assay the whole transcriptome.
Illumina's claimed specs are a maximum capture area of 15 mm by 50 mm with 1 µm resolution. 10x's new Visium HD offers two areas of 6.5 mm by 6.5 mm per slide with 2 µm by 2 µm pixels arrayed in a continuous "lawn" across the capture area. 10x recommends beginning data analysis with 8 µm by 8 µm bins. Curio's Seeker offers tiles as big as 10 mm by 10 mm while Stereo-seq's standard field of view starts there and can grow to as much as 130 mm by 130 mm. Singular's spatial method also touts the ability to analyze a large area of tissue per run, with up to 10 tissue sections of 1 cm2 per flow cell and up to four flow cells per run. It can also handle FFPE tissues.
"I suspect people will be evaluating [Illumina's spatial technology] relative to the full spatial field, including imaging-based methods from Bruker, Vizgen, and 10x," the Broad's Farhi said. "Everybody is playing for the whole field. Is it going to be compatible with peoples' samples? We'll have to see."
The people most interested in the initial version of the assay "will be thinking about large-scale samples" and looking to take advantage of the method's ability to capture poly-A RNAs. That includes T- and B-cell receptor profiling as well as RNA isoform profiling, Farhi said.
Illumina's technology won't be commercially available until the first half of 2026, however. In the meantime, the Broad collaboration will offer researchers outside the organization early access through the institute's STP.
Several researchers have already gotten a chance to send in tissue samples to be prepared and analyzed by Illumina.
"I was impressed with the overall sensitivity, as well as the large capture area," said Nicholas Banovich, a researcher and spatial biology expert at the Translational Genomics Research Institute (TGen), who sent in lung tissue samples. His lab has profiled pulmonary fibrosis with both single-cell and spatial approaches. "Looking with an untargeted whole transcriptome over a large capture area allowed us to dig in deeper," he said. The data he got back showed "relatively high UMIs per gene and high overall transcripts."
Jasmine Plummer, director of the Center for Spatial Omics at St. Jude's Children's Research Hospital, said in a statement that her lab was able to profile millions of cells from prostate cancer samples across two runs and found biomarkers that were not picked up by targeted approaches. "This improved transcript coverage allows the ability to drive rare cell type analyses, and these rare cell types were found to correlate to disease states within prostate cancer subgroups," she said.
Illumina's Segale said the assay can provide up to around 10,000 reads per cell, though "that's a pretty rough estimate with a big plus-minus there. You could certainly do less."
Barnard noted that the total capture area can fit as many as 7 million cells, though a more typical experiment might have 1 million to 2 million cells.
"We've built in a lot of flexibility," Segale said. "You can put on a small piece of tissue or pack in a lot, and you could sequence to different depths," depending on what the experiment calls for.
Informatics is a key piece of the puzzle, Barnard and Segale said. Illumina will be launching a new cloud-based software suite for multimodal analysis. Segale noted that Illumina will be using artificial intelligence-based algorithms to do cell segmentation. "We're not just applying an X-Y grid to the surface," he said, which improves delineation between cells.
The algorithms have been trained on a variety of tissue types and are able to accurately find nuclei and estimate cellular borders based on anisotropic expansion, according to the firm.
"I think the big thing that everybody is going to be anxious to see is how the company handles the transition to FFPE samples," Farhi said. Most clinically interesting samples are formalin-fixed paraffin-embedded, and other companies have invested a lot to get their spatial platforms to work with FFPE samples.
It's "the clear next step" in development, Segale said, though Illumina is also "well positioned" to add other analytes, namely proteins, in the future.
For now, Illumina is not disclosing the price of its platform and technology, and Farhi said Broad has not yet determined pricing for external researchers.
Barnard said Illumina expects its assay to be "two to four times less [expensive] than what's on the market today," based on cost per mm2, and will factor in the total cost of the experiment, including bioinformatics. "It's going to come out as disruptive," he predicted.