This story has been corrected to fix the number and dimension of tissue sections that can fit on a Singular G4X flow cell.
NEW YORK – New platforms and chemistries from Singular Genomics and Element Biosciences promise to turn their respective sequencing instruments into more than just DNA base readers, adding multiple analytes and, in Singular's case, spatial context.
At the Advances in Genome Biology and Technology meeting in Orlando, Florida, last week, Element Cofounder and Chief Technology Officer Mike Previte shared data on how the Aviti24 multiomic analysis platform, announced last month, enables in situ analysis of DNA, RNA, proteins, and morphology for up to 1.3 million cells per flow cell within the same sequencing run.
Singular, meanwhile, used the meeting to unveil the G4X, an upgraded version of its sequencer that can also do direct RNA sequencing, RNA transcript detection, multiplex protein analysis, and digital H&E staining, all on human tissue sections. With a kit that is still in development, G4X will also be able to offer cell segmentation to approximate single-cell analysis.
Sample throughput and the two-in-one nature of the platforms are major selling points for both firms, but other advantages, while potentially interesting, are not as clearly defined.
With the spatial transcriptomics field in flux, how they answer open questions about the platforms could go a long way to gaining users. For now, it could also be a way to differentiate themselves from Illumina, which appears to be content to pursue its own concept of using a sequencer to offer multiomics.
In some sense, next-generation sequencers have always been doing imaging-based spatial analysis, except the analytes have been arrayed, artificially created colonies of DNA fragments rather than biomolecules in a living cell.
Element and Singular are also not the first to go public with turning a sequencer into a multiplex protein analysis platform. In 2022, researchers from the New York Genome Center described their efforts to repurpose decommissioned Illumina HiSeq 2500s into multiplex spatial proteomics platforms.
According to both firms, they have not had to make major changes to their existing instruments to turn them into multiomics machines. Element Cofounder and CEO Molly He said the Aviti24 is more or less "the same exact instrument" as the vanilla Aviti, but with hardware and software upgrades.
"When we started Element, we wanted to go beyond sequencing," He said in an interview on the sidelines of the conference. "We started out with a sequencer, but with the vision that this same sequencer could be used for other types of molecules."
For instance, when developing the surface chemistry for Aviti sequencing, the company made sure that the technology was flexible and extendable to a variety of assays, He said.
Element's multiomic cell analysis assay on the Aviti24, dubbed Teton, requires roughly 30 minutes of hands-on time and takes less than 24 hours to run, Previte said.
The Teton flow cell has the same format as the one used for DNA sequencing, and the Aviti24 instrument can run two of them independently. Because Element's flow cells are not patterned, they can also be subdivided by a cassette to accommodate up to 12 samples per flow cell.
Using Teton, researchers can analyze up to 350 RNAs, up to 50 proteins and phosphorylated proteins, and up to 20 cell morphology features. Additionally, the Aviti24 can achieve 100 bp reads with in vitro 3D ABC (avidity base chemistry) sequencing.
In one benchmarking experiment using cell line samples, Previte showed that the platform detected RNA targets associated with kinases, the cell cycle, and apoptosis just as well as bulk RNA-seq and single-cell RNA-seq did. The platform also showed high sensitivity, comparable to that of fluorescence in situ hybridization (FISH), he added.
A poster presented by Element scientists at AGBT suggested that they could "sensitively detect" changes in mRNA in response to metabolic stress and cytokine regulation, showing 60-fold changes over a range of five to more than 1,000 copies per gene, per cell.
For protein detection, the company said the Aviti24 assay's antibody probes achieved over 90 percent agreement with benchtop methods such as immunohistochemistry in terms of subcellular colocalization. The Aviti24 cell morphology assay also enabled more features and organelles to be imaged simultaneously than a standard cell painting assay. Finally, company researchers achieved direct sequencing of V(D)J segments in captured T lymphocytes.
Previte said the company is interested in developing more multiomic assay kits moving forward, such as those for studying systems biology pathways, but he declined to offer further details. CEO He said the company "would love to collaborate with key opinion leaders or [other] companies who are interested in using Aviti to explore their own biological problems."
"I'm interested enough that I want to see more data," said AGBT attendee Marie Adams, genomics core director at the Van Andel Institute in Michigan, adding that she still has a string of questions regarding Aviti24, such as the instrument's cost and performance compared to standalone multiomic analysis platforms.
"What is your trade-off for being able to process lots of samples? Is it a decrease in resolution where, if I'm looking at a neuron, I'm going to have a hard time telling where my neuron boundaries are?" Adams said. "[The company] did not quite give enough details to tell."
Like Element, Singular is also offering an upgraded, two-in-one instrument. The big difference is that the G4X can process formalin-fixed, paraffin-embedded (FFPE) human tissue sections and offer single-cell-level spatial information.
This is a departure from the firm's earlier plans to launch a separate instrument, to be called PX, for spatial analysis.
"We started in cells early on with the PX, as they are easier to work with in proving out the methodology and were well suited to the plate-based configuration. Over the last four to five years, we evolved our methods to work in tissue, in addition to cells, with a focus on FFPE samples," Singular CEO and Cofounder Drew Spaventa said in an email.
One aspect of the PX system that is being ported over to the G4X are punch tools used to cut out tissue sections and help transfer them onto the flow cells. "You can do this at high, high throughput, and it's really gentle on the tissues, which is also critical," VP of Marketing Darius Fugere said, noting that the punches seem to help avoid issues from other manual methods of handling tissue sections, such as being ripped by tweezers.
The change to FFPE samples is at least partly driven by the set of applications available when using such tissue samples, according to CSO and Cofounder Eli Glezer.
"There's a huge opportunity to advance medicine if you can tap into the archives of well-annotated clinical tissue samples and make new discoveries," he said. "You can ask questions like, 'Why did some patients respond to a cancer immunotherapy while others didn't?' You can look at the cells in the tumor microenvironment in their intact spatial context and examine the gene transcription, protein expression, cell interactions, and even look at specific mutations at the same time. And importantly, for the first time this can be done at a scale that will support large clinical studies."
Singular's immuno-oncology-focused spatial multiomics assay will offer a 300-gene RNA panel and a panel of 10 to 15 proteins.
"We are also developing the capability to directly sequence the receptors in the T cells and B cells that are involved in the immune response," Glezer said.
Each flow cell can fit up to 10 tissue sections with an area of 1 cm2 or 32 4 mm by 4 mm sections. It can also process a range of other sample sizes and numbers. Running four flow cells at a time, each instrument run can analyze a total area up to 40 cm2. "You can go from sample to discovery in three days," Fugere said, noting that one competing high-resolution spatial multiomics platform, which he did not name, runs two slides at a time. That platform is likely the 10x Genomics Xenium: Each slide can cover up to 236 mm2 while runs take approximately two to five days, depending on panel and slide size, plus sample prep, which can take two days.
"The throughput is a very interesting point that's going to make a difference in whether people decide to go for it or not," said Toon Swings, a technology expert at Belgium's VIB Tech Watch team, which evaluates new platforms for its researchers. Run time is generally too long for many clinical trials to consider using spatial omics platforms, he noted.
If the data quality of the G4X is comparable to that of other firms, that could spur competition with spatial transcriptomics-centric platforms. The 300-gene RNA panel is par for the course in terms of what people expect such a platform to be able to do, he noted.
The ability to directly sequence DNA and RNA molecules, such as CRISPR guide RNAs in screening experiments, is another potential advantage, he said, noting that Xenium cannot read guide RNAs. "That seems to be pretty unique in the space. We for sure are interested in the combined platform" from Singular Genomics, he said.
Singular is offering the G4X as part of an "early adopter package" that will also include training, $50,000 in spatial sequencing services, and $50,000 in starter reagents. This package can be had for $400,000 by the end of Q1, going up $50,000 every quarter for the next two quarters, and upgrades should come in Q4.
Element did not publicly disclose the list price for the Aviti24, nor the upgrade charge for existing customers. It also did not provide an exact timeline for the platform's shipment, other than noting that the instrument would be available in the second half of the year. It also did not share technical details of the Aviti24 assays in greater detail.
While prospective Element customers can purchase a new Aviti24 platform, existing users can request a field upgrade of their Aviti's hardware and software to enable the same multiomic capabilities, He noted.
Fellow San Diego-based sequencing firm Illumina does not appear to be headed in the same direction as Element and Singular, staying the course with its previously announced multiomics plans, namely, to develop Illumina Protein Prep, an NGS-based version of the SomaScan assay from SomaLogic, now part of Standard BioTools.
In a poster at AGBT, Illumina researchers described early results of a 7,289-plex panel targeting 6,402 proteins in human plasma or serum samples. "Illumina Protein Prep, which generates highly multiplexed protein measurements using Somamers with a scalable NGS readout, was able to robustly detect 94 percent of the targeted content, corresponding to 6,057 unique human proteins," an Illumina spokesperson said in an email. "The median total assay coefficient of variation was determined to be 9 percent for both plasma and serum samples, and a high correlation between Illumina Protein Prep and the SomaScan Assay (with array readout) was demonstrated."
Illumina is launching the product in early-access limited release sometime this year and said it expects full commercial release of a 11,500-plex panel in early 2025.
Moreover, CEO Jacob Thaysen discussed the topic of multiomics last week on a call with investors following the release of Illumina's fourth quarter and 2023 financial results.
"We have an intention also to be in that space," Thaysen said. Earlier this year, for example, the firm announced the acquisition of a multimodal bioinformatics company, Partek. Illumina will continue to invest in multiomics, he said, but did not offer any specifics.
Illumina Protein Prep will be the starting point, but "we believe there are many more modalities that can be available on the instrument," he said.