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Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements, including major technological improvements and the introduction of new platforms. These developments were prominently displayed at this year’s American Society of Human Genetics (ASHG) conference, where Pacific Biosciences (PacBio) introduced several notable innovations, including a new instrument, Vega.
“Vega is PacBio’s first HiFi benchtop sequencer,” explained Aaron Wenger, Senior Director of Product Marketing at PacBio. “We're really aiming for broad accessibility—to be in labs that are interested in HiFi sequencing but not able to handle the initial costs.” Wenger highlighted that the instrument is compact (2 ft x 2 ft), designed to operate with standard lab power and internet, and comes with two purchasing options to further increase accessibility. Vega also works in tandem with PacBio’s flagship Revio system, addressing the diverse needs of researchers while sharing the same ecosystem. “Both systems have the same upstream library prep and produce the same rich data type,” Wenger added. While Revio remains the choice for large-scale genome projects and clinical labs, Vega offers a solution for smaller-scale tasks or research and development without disrupting larger workflows.
The launch of Vega was complemented by the introduction of SPRQ chemistry on the Revio system. This new SPRQ chemistry reduces DNA input requirements four-fold, from micrograms to nanograms, while significantly boosting the sequencing output per cell. “DNA input was a big challenge for many folks,” stated David Miller, Vice President of Global Marketing at PacBio. “For the last several years, we've really focused on how to knock that barrier down.” The development of SPRQ chemistry is the culmination of these efforts. Miller noted that SPRQ chemistry leverages an enhanced sequencing polymerase and offers higher sequencing outputs, all without increasing reagent costs.
PacBio also announced developments in multiomics capabilities alongside its sequencing systems. The enhanced methylation analysis offered by Vega and Revio now includes improved 5mC accuracy and the ability to analyze 6mA methylation, enabling popular assays like Fiber-seq. “That brings us to our goal of delivering a multiomic portfolio,” stated Wenger, noting how researchers can obtain accurate phased genomes, methylation data, and chromatin accessibility all from the same experiment.
To improve accessibility, Miller highlighted PacBio’s collaborations with partners like Volta Labs for automated library preparation and DNAstack for simplified data analysis. He noted that these partnerships aim to ensure that the technologies are accessible and efficient for diverse applications. Additionally, the release of new sample preparation protocols, such as saliva-based DNA extraction, is making HiFi sequencing feasible in remote and resource-limited settings.
“The future will likely see long-read sequencing becoming the standard for comprehensive genomic analysis, especially in applications requiring detailed exploration of structural variants, gene expression, and disease-associated mutations,” stated Miller. He believes PacBio’s ongoing innovations are driving this shift, enabling long-read sequencing to transform a wide range of scientific and medical fields.
Single-Cell Sequencing
Single-cell sequencing is another area of steady innovation, and Scale Biosciences (Scale Bio) is among the groups making significant progress. Jason Koth, Senior Product Manager at Scale Bio, noted that traditional single-cell methods often restrict researchers to analyzing a fraction of their samples, limiting statistical power. Scale’s technology addresses these limitations by allowing the profiling of up to 500,000 cells simultaneously, lowering per-sample costs, flexibly multiplexing hundreds of samples in a single workflow, and employing a fixation method for sample storage and batch processing. “Our technology opens the door to more comprehensive, statistically robust experiments that can reveal subtle cellular variations and rare cell populations that might otherwise go undetected,” stated Koth.
Scale Bio continues to innovate in single-cell analysis, and Koth pointed to three notable advancements. Their Single Cell Methylation Sequencing kit enables high-throughput, whole-genome methylation analysis, utilizing parallel barcoding and sample fixation to profile thousands of single-cell methylomes. The ScalePlex multiplexing technology allows researchers to process and demultiplex hundreds of samples efficiently, while significantly reducing hands-on time. Additionally, their new QuantumScale platform supports profiling up to 2 million cells in a single run, integrates with ScalePlex for multiplexing, offers high cell recovery rates, and preserves samples for up to a year with fixation. Koth described these innovations as “game-changers,” transforming the scale and precision of single-cell studies.
The most thrilling aspect of single-cell sequencing, Koth noted, is its potential to reshape how diseases are understood and treated. “By enabling researchers to profile more cells and samples than ever before, we’re moving the needle from analyzing subsets to potentially performing single-cell analysis on every sample in a study.” The applications of this technology have been diverse with its use in neurodegenerative disease research for identifying genetic factors behind conditions like Alzheimer’s and Parkinson’s, and drug discovery, facilitating extensive gene pathway analysis for identifying drug targets.
The formation of various collaborations has also played a role in Scale’s progress toward greater technology access. Their partnership with Ultima Genomics integrates Ultima's advanced sequencing technology with Scale Bio’s QuantumScale platform to enable cost-effective, large-scale single-cell studies, including routine million-cell experiments. Collaborations with SPT Labtech and Miltenyi Biotec include automation for RNA sequencing on the Firefly platform and tissue preparation with the gentleMACS™ instrument. “These collaborations underscore our commitment to providing comprehensive, end-to-end solutions that address every aspect of the single-cell workflow, from sample preparation to sequencing and analysis,” emphasized Koth.
3D Genomics
The study of 3D genomics, which explores the spatial organization of the genome within the nucleus, is a rapidly growing area of research. Ibrahim Jivanjee, Senior Director of Product Management and Marketing at Arima Genomics, explained that recent innovations have deepened our understanding of genome organization, gene regulation, structural variation, and their implications in biological processes and diseases.
Discussing Arima’s contributions, Jivanjee detailed how their 3D genomics tools have driven significant discoveries. For instance, their single-nucleus methyl-3C sequencing (sn-m3C-seq) technique captures DNA methylation and chromatin conformation in single cells, allowing researchers to identify cell-type-specific regulatory mechanisms by linking chromatin interactions with differential DNA methylation patterns. “This technique, employed by members of the scientific community such as the Ecker Lab at the Salk Institute as part of the BRAIN initiative, has enabled the creation of a comprehensive cell atlas of the adult mouse and human brain,” stated Jivanjee. By profiling DNA methylation and chromatin conformation at single-cell resolution, researchers have revealed cellular diversity and complex regulatory landscapes in the brain, filling gaps left by current multiomic techniques.
Another notable development is the expansion of 3D genomics into translational and clinical research, particularly in oncology. “These methods have proven valuable in detecting structural variants such as genomic rearrangements and gene fusions that are detected by gold-standard clinical methods, but importantly, those that may be missed, including those in challenging Formalin-Fixed Paraffin-Embedded (FFPE) samples,” stated Jivanjee. Furthermore, Hi-C analysis has played a significant role in revealing extrachromosomal DNA (ecDNA) and its impact on tumor development and drug resistance. These techniques hold promise for improving biomarker identification, diagnostics, and patient management.
The integration of Hi-C data with long-read sequencing technologies has improved the accuracy and completeness of genome assemblies by resolving complex and repetitive regions and supporting haplotype phasing. Jivanjee noted that projects like the Vertebrate Genomes Project, the Darwin Tree of Life project, and the European Reference Genome Atlas have leveraged this integration to produce high-quality genome assemblies. “The long-range contiguity information in 3D genomics data provides this missing layer of insight, facilitating chromosome-scale and haplotype-resolved assemblies,” he explained.
Stressing its importance, Jivanjee expressed his group’s excitement about the clinical prospects of 3D genome technology. In collaboration with several clinical labs around the country, Arima Genomics has demonstrated the clinical potential of 3D genome technology through a retrospective analysis of 243 solid tumor samples that lacked actionable variants after conventional genomic profiling. Their methods identified actionable gene fusions or rearrangements in 13% of patients, with additional variants detected in 9% linked to other diseases and 1% targeted by ongoing clinical trials. These findings emphasize the ability of 3D genomics to identify more actionable insights and have led to the launch of the Aventa FusionPlus test for solid tumors.
Looking ahead, Arima plans to simplify data integration and expand clinical applications through its CLIA-certified lab. These efforts aim to broaden access to 3D genomics technology and its potential to impact patient care.
Innovations in Sequencing Platforms
Over the past year, the field has witnessed several other important technology releases. Illumina introduced the MiSeq i100 Series, a successor to its workhorse MiSeq platform, which has been a staple in the market for over a decade. The MiSeq i100 and i100 Plus were designed to provide same-day sample-to-analysis with room-temperature reagent storage, reducing thaw times and packaging waste. Other key features include XLEAP-SBS chemistry, rapid four-hour run times, and flexible output configurations.
Element Biosciences is preparing to launch the AVITI24 platform, which enables researchers to analyze DNA, RNA, proteins, phosphorylated proteins, and cell morphology from a single sample. Requiring less than 45 minutes of hands-on time, AVITI24 is a one-of-a-kind platform that provides comprehensive multiomic insights within 24 hours.
Singular Genomics introduced the G4X Spatial Sequence this year, which combines next-generation sequencing (NGS) with spatial multiomics. The G4X supports high-throughput in situ analysis of RNA, proteins, and morphology from tissue samples, including difficult FFPE specimens. Powered by Singular’s Direct-Seq technology, it can directly sequence variable RNA regions within cells, making it valuable for applications in cancer research, immunology, and gene editing.
Final Thoughts
These ongoing advancements in sequencing technologies are making genomics tools more accessible while also improving our ability to explore complex biological systems. With such a vast field, it's impossible to capture all the amazing changes that have occurred over the last year. What do you consider the most exciting developments in sequencing? Share some of your thoughts with the community in the comments below.