Next-Generation Sequencing October 2024

Element Bio, Illumina MiSeq i100, Ultima Genomics and GeneMind

We’ve had a busy month in Next-Generation Sequencing (NGS) and Multi-Omics (NGSX), with announcements from Element Bio, Illumina ILMN 0.00%↑ , Ultima Genomics and GeneMind as highlights.

Element Bio “Beyond” event

Element Biosciences, commonly referred to as Element Bio, is a company that entered the Next-Generation Sequencing (NGS) market in 2022. Based in San Diego, California, Element Bio was founded by a team that includes many former employees of Illumina, a leading company in the NGS field. The company aims to provide innovative, cost-effective sequencing platforms and reagents, positioning itself as a competitor in the highly competitive genomics space.

Element Bio’s flagship product is its AVITI Sequencer, which is designed to offer highly accurate sequencing at lower costs, making it accessible to a broader range of researchers and industries. The AVITI platform combines cutting-edge hardware and software innovations to deliver flexible and scalable NGS solutions. This system is geared towards democratizing access to high-quality sequencing by offering lower prices for instruments and consumables, making Element Bio a key player for small and medium labs and new markets. Meanwhile, Illumina makes most of their revenue from their $1M+ NovaSeq instruments, with the mid-throughput NextSeq and low throughput product lines making only a fraction of what the NovaSeq line makes for them.

With its roots in San Diego’s vibrant biotech scene, Element Bio benefits from the expertise and experience of former Illumina employees who are familiar with the challenges and opportunities in the sequencing industry. Their focus on innovation, affordability, and user-friendly systems has so far positioned Element Bio as a rising competitor to established short-read NGS companies like Illumina, Thermo Fisher, and MGI Tech / Complete Genomics.

The “Beyond” event started with Element’s CEO giving an intro into what the company has been doing so far, and what was on the menu for the event.

The company has been selling the AVITI mid-throughput system since 2022. This is what we can now call the 1st gen instrument, as the AVITI24 will become the second in the history of the company.

Some of the tenets of the design of the AVITI would resonate with small and medium labs, tired of the issues with large batching of samples into Illumina NovaSeq instruments. The AVITI offers flexibility, with individually addressable lanes and flowcells, and an advantageous price per Gb with an instrument that is not $1M+ CAPEX like the Illumina NovaSeqs.

As part of the presentation, several AVITI customers explained what it means for them to be able to run the AVITI, many of them having been long-time Illumina customers, directly or indirectly, tied to the cycle of large batches and having to amortize and upgrade their $1M+ machines every 5 years.

The R&D department at Element has been busy working on new products. One of the focuses was on bringing multiple data type readouts from the same sample, an evolution of the DNA-only (or cDNA-only) readouts from a single sample.

Running through some of the history of product releases so far, Matthew Kellinger gave an overview of the launch of the AVITI 1st gen, the update of the chemistry to Cloudbreak (2x150bp / 2x75bp) in 2023 reducing run times down to 20 hours.

Later came releases like Expert Mode HD, and the much acclaimed 2x300bp Cloudbreak kit, with better Q-scores to the NextSeq 2000 standard (not clear if they referred to XLEAP-SBS or previous chemistry).

The circular DNA technology that Element uses is one of the keys to their high quality low cost offering, and since everybody is used to linear DNA fragments, they releases Cloudbreak Freestyle in 2024 for a seamless workflow integration with no library conversion.

The avidity technology is one of the keys to the high quality readouts. This is a differentiator to other short-read imaging-based methods out there, including Illumina.

So much so that the company released a Cloudbreak UltraQ kit, for 2x150bp runs, which achieves Q50 scores for more than 70% of the reads.

The comparison to other companies out there should have them worried: both Illumina ILMN 0.00%↑ and PacBio PACB 0.00%↑ are claiming much improved qualities from recent products, but the AVITI UltraQ shows much better results in the graph below to the Illumina counterpart.

This “Beyond” event was an opportunity to give more details on the new product: AVITI24. There were some presentations and materials available before, but a lot of detail was given in this presentation.

The AVITI24 is able to do NGS sequencing in cells, but also able to provide readouts on RNA/Protein/Morphology for the same sample of cells affixed on the flowcell of the Teton kits.

The other big announcement was the Trinity Kit, for on-flow cell enrichment, optimizing the somewhat tedious hybridization capture methods that have been used everywhere for the past 15 years. Trinity offers remarkable time savings, great on-target accuracy compared to the other solutions.

Importantly, Element also has a ElemBio Cloud offering for downstream analysis. It only took one sentence to differentiate this offering from Illumina BaseSpace DRAGEN: ElemBio Cloud leverages widely used open-source tools, rather than reinventing them.

The company has now 300 instruments in 36 different countries, and more than 10000 runs have been completed as of September 2024. They have a strong group of Field Service engineers and Field Application Scientists, who can get to a customer in a day.

A back of the envelope calculation on the instruments and runs completed: given that most of the runs would have been performed when the install-base was around 200 instruments in a window of about 12 months, this means that the 10,000 runs divided by 200 instruments give about 50 runs per instrument, or roughly one run per week, with a 2 week holiday to spare. Considering that they could be doing 1 run per day if they did 20 hour runs, this is 1/7 of the max utilization rate, but in the history of NGS for the last 10-20 years, one run per week is not bad at all!

Illumina NextSeq machines, the equivalent to AVITI, have probably a lower utilization rate, given that their install-base is in the thousands, and make less revenue for Illumina than what a 1 run per week would do.

Another comparison is Oxford Nanopore: the company started their product offerings with the low-throughput MinION, followed by the mid-throughput GridION (5x) and high-throughput PromethION (24x times 5x per flowcell). It was later on, realising that PromethION customers were running 1 or 2 flowcells per week that ONT released the P2 Solo (and P2i) instrument, catered for the throughput that they saw the customers wanted. At $10,500 for a P2 Solo with starting kit, it is so far the unbeatable NGS offering out there when it comes to quasi-zero CAPEX for a mid-throughput NGS instrument.

Back to Element, more details on the Trinity part. The protocol can do fast hybridization with 2x75 sequencing in 1-day turnaround time, giving 1-16hr for the probes to hybridize to the sample. So one can start at 9 am, give the sample 4h 30m to hybridize, and load on the sequencer at 2.30 pm.

Importantly for enrichment protocols, the on-target rate and low duplication rates with high library complexity is crucial for a good read-out. Trinity shows better results than In Solution equivalent.

Trinity is compatible with TwistBio panels and IDT panels with standard 16-hour hybridization, with Fast hyb coming soon.

The next versions of Trinity, named Trinity Plus, will also include a low-pass sequencing readout of the entire sample together with the high coverage enrichment. This is important for applications like AgBio, human sequencing (CNV calling), infectious diseases, and Minimal Residual Disease assays for cancer (MRD).

The Trinity kits are now available for pre-order from the Element Bio website.

Now onto the Multi-Omics offering: AVITI24 and the Teton kits. It all started with the realisation that NGS sequencing by itself doesn't provide all the desired insights, so a combination of of NGS/RNA/Protein/Morphology data is a step forward for people doing their science.

The aim is to exponentially change the understanding of biological systems, and this is how the testimonials for AVITI24 and Teton describe it.

So the AVITI24 instrument can do higher throughput NGS, as an evolution of the AVITI 1st gen instrument.

But at the same time, it’s a multi-omics instrument with Teton CytoProfiling, capable of assaying 2 million cells per run on a 20cm square area per run, with a total workflow time of 24 hours, and a multiomics readout combining RNA, protein and cell paint.

The RNA readouts an include 350+ targets, the protein readout can include 50+ targets, and the morphology readout is based on 6 different markers.

The cell paint process is reversible, not limited by the imaging resolution as it is based on the avidity reactions to the cell components, like the cell membrane. This is then followed by the RNA and Protein combined read-outs, and a lot of effort went into achieving this, as RNA and Proteins don’t usually play well together with standard reagents tailored for either one or the other. Finally, ABC sequencing can do up to 3000 transcripts per cell.

All of this is offered in a simplified workflow, sample to answer in 24 hours. The cell preparation has a couple of different options, followed by the loading, wash, fix and permeabilize steps which take less than 1 hours, and once the flow cell is assembled, it is loaded on the instrument for sequencing and primary analysis, which happens on the instrument. After a total of 24 hours run time, the results are ready for Data Visualization.

The two flow cell options, either for culturing cells on the cartridge or depositing the cells directly on the Teton flow cell, are a 12-well construct, with up to 50k cells per well, or a large single well option, with up to 1M cells per flow cell.

The primary analysis happens onboard, so the results can be visualized after 24 hours of loading the sample onto the instrument.

The system is highly sensitive to the number of transcripts detected per cell.

But you don’t have to take the word from Element’s reps for this, as this can be compared to bulk RNA-Seq or scRNA-Seq readouts of the same sample.

At the low-end of the RNA expression range, we observe how both bulk and scRNA-Seq methods can miss molecules that are found by the AVITI24 system.

For the protein readout, we can compare it to immunofluorescence, and see a high correlation between the two methods.

Given that the dynamic range of protein expression can be massive, it is important to demonstrate that the AVITI24 system can detect proteins along a wide range.

The company showed examples of the CytoProfiling system, starting with a drug discovery application: cancer cells treated with a couple of different drugs, so one can observe how they react to the treatment in a multi-omics fashion.

The observation is a heterogeneous, dose-dependent cellular response to the treatment with the druge over time.

The multi-omics readout is also capable of resolving the cell cycle stated of the samples.

The different multi-omics profiles can also be overlayed on the gene network of the regulatory pathway involved in the cells assayed. This can be done over time so that the changes in gene expression are mapped out on the gene network.

Finally, the in situ sequencing, which will become available in H2 2025. They showed preliminary data, both for targetted and untargetted applications.

The results are comparable to the usual NGS standard, only this happens in situ, on the 3D imaging of the cells that are affixed to the flow cell.

And here again, not taking their word for granted, they compare the readout of the in situ sequencing with the equivalent scRNA-Seq, very impressive correlation.

The Direct ABC untargeted method can be used, for example, for 3’UTR sequencing, capable of mapping the reads onto the 3’ end of genes, thus inferring their expression levels without having to decide which genes to choose for a targeted readout. This gives 1000s of RNA counts per cell over multiple sequencing rounds.

CytoProfiling is launching with two pre-defined panels in H1 2025, but will be followed by Custom RNA and Protein panels, 48-well format, in situ sequencing in H2 2025 and expanded sample types.

One example shown was how the multi-omics readout is able to classify cells, here on a UMAP plot, as belonging to the different stages of the cell cycle. The doughnut shape is actually what one would expect: the cells keep going on in circles around the doughnut as they go around the cell cycle steps as one would expect from the definition from a biology book.

Illumina MiSeq i100

Illumina ILMN 0.00%↑ remains the dominant company in short-reads Next-Generation Sequencing, with over 90% of market share in many short-read NGS markets. They make most of their revenue from NovaSeq instruments, followed by NextSeq and finally from the low-throughput product line. Because if this, the company hasn’t had the low-throughput instruments high in their list of priorities, and the combination of the MiniSeq, iSeq100 and the original MiSeq instruments hadn’t been updated for many years.

The new MiniSeq i100 is Illumina’s solution to the product consolidation of the modern XLEAP-SBS chemistry, now in all 3 product lines.

For a detailed analysis of the MiSeq i100 launch, read my post here.

Ultima Genomics

Ultima Genomics has announced the placement of several of their UG100 instruments in different territories. The UG100 had been announced a while ago, first with an announcement 2-3 years ago and later with another one, including a visit to the facilities for a select group of experts, about a year ago. Now the company has started installing UG100s and making this technology, the only one aiming at $1/Gb in the Western old, available for the first time.

GeneMind

A third company with aspirations in NGS is GeneMind. Based in China, they have so far flown under the radar, with MGI Tech dominating the headlines for NGS in China and the sphere of influence.

But GeneMind announced recently their GeneMind SurfSEQ Q instrument, an attempt to challenge the Illumina NovaSeq and the DNBSEQ-T7 from MGI Tech.

The only specs we know is that most of the reads/bases are above Q40 (>90%) and that it can produce 9 Terabases of data in 24 hours.

The question remains as to how available this instrument, and any instrument from GeneMind or MGI Tech, will be to customers in the Western world.