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This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
The Headliner
The biggest announcement was Roche stepping back into the sequencing platform market. In the years since Roche stopped supporting their 454 instruments, they continued to produce library preps, library quantification kits, and automation systems for other devices. Roche’s long-awaited Sequencing By Expansion (SBX) technology was revealed in a comprehensive webinar the week before the conference. Details about current metrics can be found on Roche’s site, and a new pre-print explains the principles of SBX technology.
During AGBT, Roche shared sequencing performance data from projects with the Hartwig Medical Foundation and the Broad Institute. The Hartwig Medical Foundation evaluated SBX sequencing for whole-genome cancer diagnostics and achieved a 24-hour turnaround with data quality and variant detection comparable to Illumina’s NovaSeq 6000. Additionally, the Broad Institute assessed SBX for rapid clinical applications, such as neonatal ICU diagnostics, and research applications like single-cell RNA isoform sequencing and multiomics drug-response profiling. The results demonstrated the sequencer's potential for rapid and precise applications.
Roche plans to launch the SBX sequencer as a research-use-only product in 2026. While initial reactions to the new instrument are generally positive, questions still linger about pricing, scalability, and performance beyond early-access laboratories.
Biology in the Third Dimension
Though still a relatively young field, spatial biology has significantly matured, as evidenced by numerous applications and industry announcements shared at the meeting. Bruker captured attention with their extensive technology updates and the presentation of innovative research enabled by their instruments.
Among Bruker’s announcements was the release of a Whole Transcriptome Panel (WTX) for the CosMx Spatial Molecular Imager (SMI) platform, which can detect and quantify over 18,000 RNA transcripts at single-cell and subcellular resolution. Bruker also introduced the PaintScape platform for direct visualization of the 3D genome, such as chromosomal structure and genome architecture in single cells. Furthermore, the company launched the PowerOMX software engine for the CellScape spatial proteomics platform. The software engine improves upon their advanced photobleaching technology, EpicIF (Enhanced Photobleaching in Cyclic Immunofluorescence) to optimize data acquisition, processing, and reconstruction. The GeoMx protein panel also received a significant expansion with the ability to perform 1,000-plex experiments.
Illumina surprised researchers by announcing their own spatial technology that is compatible with their current sequencing instruments. This new multimodal platform offers whole-transcriptome profiling with high sensitivity and resolution. Data from collaborations with organizations like the Broad Institute showcased its potential in disease research, with a planned release in 2026.
Another interesting development in spatial biology was the entrance of newcomers like Stellaromics. Their 3D profiling platform, Pyxa, distinguishes itself by effectively analyzing thicker tissue sections (100μm or greater) without sacrificing sub-cellular resolution. “The concept of our company is to bring spatial into the third dimension,” stated Todd Dickinson, Ph.D., Chief Executive Officer of Stellaromics. Rather than relying on traditional two-dimensional tissue slices, Dickinson emphasized that Pyxa preserves intact cellular structures, uncovering rare cells, and providing richer, more accurate biological insights.
Stellaromics was spun out of Karl Deisseroth’s lab at Stanford and Xiao Wang’s lab at Broad and utilizes some of their pioneering techniques to visualize tissues in 3D. Dickinson explained that Pyxa’s 3D imaging capabilities are driven by three key technologies. The first is a hydrogel chemistry that is essential for tissue clearing and enhanced imaging. Second is the assay, which generates strong signals, minimizes background noise, and uses amplification techniques to improve signal clarity. Lastly, the third component is the instrument and hardware, designed for high-speed, confocal imaging.
In addition to their core technology, Dickinson emphasized that their assays like RIBOmap deliver unique perspectives on samples. This assay employs a ribosome-binding probe to detect actively translated RNAs, allowing researchers to study translation and transcription. While Dickinson noted that Pyxa complements other spatial platforms, the company plans to scale their technology and expand its range of applications. Early adopters are already utilizing Pyxa in numerous applications, and its early access program is scheduled to launch in the second half of 2025.
The Age of Multiomics
Single-modality instruments and assays are becoming a thing of the past and being replaced by more comprehensive solutions. Element Biosciences demonstrated this concept during the meeting with AVITI24, their newest benchtop instrument that integrates high-throughput sequencing with multiomic in situ analysis for simultaneous DNA, RNA, protein, and cell morphology profiling. “We wanted to build the ultimate biological assay where it’s sample in, answer out,” stated Michael Previte, Ph.D.,CTO, SVP of R&D, and Co-Founder of Element Biosciences. Previte emphasized that AVITI24’s workflow requires minimal manual intervention and integrates high-resolution imaging, fluorescence detection, and adaptable surface chemistry for a streamlined multiomics analysis.
Before the meeting, Element shared their upcoming roadmap for AVITI24 which includes new Teton panels for immuno-oncology and neuroscience, expanded protein profiling options, broader sample compatibility, and a high-throughput 48-well slide kit for AI-assisted analysis. Later in the year, advancements will include direct sequencing from samples without library preparation and a custom workflow builder for optical pooled screens and protein analysis. “The most exciting thing is the direct in-sample sequencing,” stated Previte. Eliminating the need for complex library preparations, this advancement allows for real-time RNA and protein profiling in cells. Previte believes AVITI24 represents the next major step in biological assays and sequencing, and he noted that future developments will expand the instrument’s capabilities and applications in both research and clinical settings.
Single-Cell Expansion
Single-cell sequencing remained a major discussion point during AGBT, with Scale Biosciences (Scale Bio) and Parse Biosciences increasing adoption through cost-effective, instrument-free approaches.
Scale Bio kicked off the meeting by announcing the availability of their QuantumScale Single Cell RNA Kits. Giovanna Prout, President and CEO of Scale Bio, explained that this innovation lowers the cost of single-cell research, making it accessible to smaller and underfunded groups while also supporting large-scale experiments. In addition, the new Quantum Barcoding technology streamlines plate-based workflows by compressing barcode generation, which reduces steps and variability. The workflow utilizes plates embedded with micro-wells for flexible cell loading and beads for barcode application. This approach continues to evolve, as Prout noted, and offers the potential for larger bead pools, denser micro-wells, and the ability to process 5, 10, or 20 million cells with the same streamlined workflow.
Prout also emphasized the real-world applications of Scale Bio’s technology, including an innovative study by David Rincón from Cedars-SinaiMedical Center, who used single-cell methylation to identify drug targets for pediatric gliomas. Another recent milestone for Scale Bio was the generation of a massive one-run mouse brain dataset, where AI from Panacent Bio enhanced cell annotation and reduced sequencing costs. Lastly, Prout underscored the significance of strategic collaborations with Ultima Genomics, NVIDIA, BioTuring, and the Chan Zuckerberg Initiative (CZI) for the 100 Million Cell Challenge. The initiative generated massive interest, attracting nearly a billion cells' worth of proposals from over 140 projects worldwide. The CZI fully funded 50 million cells, providing researchers early access to QuantumScale technology. The selected winners are now working with Scale Bio to optimize experiments for sequencing on Ultima's platform.
During their sponsored talk, Charlie Roco, CTO and Co-Founder of Parse Biosciences, highlighted the company’s key developments. Roco shared Parse’s rapid expansion and announced the launch of Evercode WT Penta and Penta 384, which allow researchers to analyze 5 million cells and 384 samples per run. Other notable innovations from Parse include the Mouse BCR and Transgenic Mouse BCR to enhance antibody discovery and immunology research. The team also shared successful partnerships with Ultima Genomics and Vevo Therapeutics and presented a recent preprint featuring an extensive single-cell atlas with 100 million transcriptomic profiles generated through their platform.
Advances for Library Preparations and Epigenetics
The impact of enzyme engineering is often underappreciated, yet it has rapidly advanced sequencing, sample preparation, and our understanding of RNA and epigenetics. These advancements were reflected in the latest innovations from groups like New England Biolabs (NEB), which used the meeting as an opportunity to highlight the strong performance of several new products, including their enhanced UltraExpress DNA and RNA Library Prep Kits. Andrew Barry, Associate Director of Product Portfolio Management at NEB, explained that these kits align with the trend of faster workflows, increased streamlining, fewer steps, reduced cleanups, and minimal enzymatic additions. He pointed out that, in addition to producing high-quality results and optimizing workflows, these kits are designed to handle varying sample concentrations under uniform conditions, making them automation-friendly and helping to reduce consumable waste.
Similarly, the team showcased the advantages of their NEBNext Enzymatic Methyl-seq v2 (EM-seq v2) Kit. Chaithanya Ponnaluri, Manager of NGS Development at NEB, shared that EM-seq v2 integrates with NEB’s UltraShear system to improve methylation sequencing by extending the input range, eliminating acoustic shearing, and enhancing FFPE sample compatibility. NEB is also developing solutions for long-read sequencing, including tunable enzymatic fragmentation to produce molecules up to 20kb, useful for genome phasing and assembly. Additionally, the group developed a direct RNA sequencing kit for Oxford Nanopore Technologies (ONT), featuring NEB’s Induro reverse transcriptase, which ONT now recommends for superior performance.During the meeting, NEB also introduced an upcoming low-bias small RNA kit, designed to improve the detection of challenging RNA species, such as microRNAs (miRNA) and piRNAs. Dr. Ponnaluri noted that the kit supports a broad input range, overcomes ligation-based limitations, and enables multiplexed sequencing for high-throughput applications.
Watchmaker Genomics presented their latest advancements in epigenetic sequencing with the market debut of their TAPS (TET-assisted pyridine borane sequencing) technology. Trey Foskett, Chief Executive Officer of Watchmaker Genomics, explained that TAPS is an innovative sequencing technology that enables direct, high-fidelity methylation mapping. Unlike conventional bisulfite sequencing, TAPS reduces template damage and noise, thereby preserving genomic complexity and increasing the statistical power of the assay. TAPS also improves oncology screening and biomarker discovery by enabling detailed epigenetic variation detection with minimal sample destruction and lower input needs (0.5ng–200ng), making it well-suited for cfDNA applications.
Watchmaker is also introducing Equinox Prime, an updated version of their Equinox Library Amplification kits. Foskett stressed that amplification is a critical step and that the team was focused on overcoming polymerase slippage to produce a product with low error rates and base misincorporations, supporting MSI calling and oncology applications. The group also teased an upcoming library normalization kit. While normalization is an arduous and time-consuming task, Foskett shared that they have a novel approach to that is non-destructive, scalable, and enables a broad range of inputs. Finally, Watchmaker is planning to expand their molecular diagnostics portfolio with innovations such as RPA (recombinase polymerase amplification)for isothermal amplification.
Among the library prep advancements highlighted at AGBT was the early access launch of seqWell’s MosaiX Library Prep Kit. Designed for human population genomics applications like whole exome and whole genome sequencing, MosaiX utilizes seqWell’s TnX transposase to improve activity, minimize insertion-site bias, and complete workflows in just 90 minutes. With directional tagmentation, the updated MosaiX chemistry delivers high-complexity, uniform libraries. Meanwhile, seqWell launched early access to PhiRx, a spike-in control library that enhances color balancing and demultiplexing on Illumina's XLEAP-SBS system. PhiRx corrects color imbalances to recover lost sequencing data, which reduces undetermined reads and improves run performance.