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Part II of AGBT continued…
Illumina
Illumina’s most anticipated talk clarified their new long-read sequencing methodology known as Illumina Complete Long Reads (CLR). Many customers were unaware if this new technology would require modifications to existing instruments or if the method involved synthetic long reads.
The company’s presentation showed that the CLR process begins with the tagmentation of the DNA, which normalizes the long fragment sizes. These fragments are landmarked to capture single molecule, long read information, and then the molecules are amplified. Long fragments containing the landmarks are then tagmented again to become the standard size for short-read sequencing libraries. After sequencing, the landmarked regions are used to assemble the long reads. An image of the process from Illumina’s CTO can be seen here.
Much of Illumina’s main efforts during the meeting were centered on promoting the success of their newest pair of sequencers: NovaSeq X and X Plus. After announcing the release of the instruments last September, they successfully shipped their first sequencer to the Broad Institute. Illumina officials and star customers presented data comparing the results against the older NovaSeq 6000. Key metrics like consistently high Q-values throughout the entirety of the run were shown to highlight the improvements.
Final presentations from Illumina explained the upgrades and performance of their popular NextSeq 2000. The new chemistry, XLEAP-SBS, will be available later this year with their designated P4 flow cell, while compatibility with other flow cells and kits will be accessible in the future.
Bio-Rad Laboratories
Bio-Rad presented results during the meeting highlighting updates to their SEQuoia RNA Sequencing Library Preparations. Collaborating with Singular Genomics and Element Biosciences, the popular kits are now compatible with their respective G4 and AVITI sequencers. This update was part of the company’s concerted efforts to make these high-performance kits accessible to users regardless of the platform. Bio-Rad also showcased the SEQuoia Complete Kit’s ability to perform comprehensive transcriptome profiling of low-quality FFPE samples.
Another important announcement for Bio-Rad was the release of their QX600 Droplet Digital PCR System, which was designed for quantifying multiple targets with enhanced accuracy, reproducibility, and sensitivity. The company displayed the QX600 System alongside their CFX Opus Deepwell Real-Time PCR System for conference attendees.
Element Biosciences
Talks from Element Biosciences emphasized the updates and direct applications of their AVITI sequencing platform. Since their first shipment of AVITI in May of 2022, Element has provided many upgrades to their instrument with hints of more big updates in the future.
Matthew Kellinger, VP of Biochemistry and Co-Founder, gave details about Element’s new Cloudbreak chemistry. With an expected release in April, Cloudbreak significantly reduces sequencing times while increasing accuracy. The cost of sequencing with this new chemistry is an estimated $200 a genome, or $2 per gigabase.
During the meeting, Element also introduced the Elembio Cloud Platform (ECP). This software portal allows users to configure and manage their instruments and user access, as well as
monitor their sequencing runs remotely.
Several other presentations covered the direct benefits of avidity sequencing and the application of the technology in single-cell research, cancer genomics, and metagenomic analysis. Direct comparisons against competitors’ instruments supported Element’s message of lower costs with high-accuracy sequencing.
10x Genomics
10x Genomics, single-cell sequencing and spatial biology provider, showcased several unique instruments. Their new Chromium Flex was shown to provide quality data with samples that are fresh, frozen, and FFPE tissue. The increased scalability of the Flex allows users to process millions of cells and hundreds of samples in a single experimental run.
Their Visium CytAssist instrument, which simplifies their Visium spatial discovery platform, was presented to include more advantages and capabilities. The device will have increased compatibility with different sample types and doesn’t require tissue optimization. In addition, 10x Genomics is preparing to launch the ability to co-detect protein expression and genes from the same FFPE tissue section. Data from the new Visium HD showed whole transcriptome discovery from whole tissue sections at single-cell scale resolution.
Updates to the Xenium In Situ platform were also covered at the meeting. The company provided a roadmap that demonstrates the future directions for the platform. This roadmap includes a 5,000 plex multi-tissue gene panel on seven human FFPE tissues, multimodal cell boundary stains with a trained cell segmentation algorithm, multiplexed RNA and protein on the same section, and isoform mapping and SNV detection.
Spatial Biology
The continued expansion and popularity of spatial biology products was evident at the conference. Vizgen, Akoya Biosciences, NanoString, and 10x Genomics all presented their instruments along with their unique aspects.
NanoString stood out as the Gold Sponsor for the meeting, and their GeoMx and CosMx platforms exhibited their multiplexing abilities.
The MERSCOPE from Vizgen was demonstrated to perform high-quality data and the simultaneous detection of RNA and proteins.
Akoya Biosciences’ PhenoCycler-Fusion also showed multi-omic (protein and RNA) work in addition to clinical applications.
Finally, 10x Genomics presented their new directions with Xenium in their roadmap as previously mentioned.
Individual Presentations
Last but certainly not least, AGBT was packed with talks covering the extraordinary work being done across the field of genomics. Below are only a few of the notable talks given.
• Karen Miga focused on her efforts with long-read sequencers and their ability to push the limits of complete, accurate genome assemblies. The data presented showed the results from her trials with PacBio’s HiFi and Oxford Nanopore Technologies’ (ONT) duplex reads. Slides for her talk were kindly uploaded here.
• Heonseok Kim demonstrated a multiplex CRISPR editor with an ONT long-read sequencing method. This allowed for gene expression and variation detection within the same cells to examine variants of unknown significance.
• Beth Shapiro gave a talk on her genetic studies of bison, past and present, along with the interesting history of ranchers interbreeding cow and bison to produce beefalo.
• Chris Mason spoke about his team’s work on the Spatial Atlas of Human Anatomy (SAHA) Project. This is a collaboration between NanoString Technologies and Weill Cornell Medicine to create a high-content spatial map of the human body.
• Alex Cagan presented his work on somatic evolution across the tree of life. He explained how spontaneous deamination, endogenous errors, and reactive oxygen damage lead to somatic mutations in mammals.
• Pardis Sabeti talked about her work on Sentinel (a pandemic preemption system) and covered her experiences monitoring deadly outbreaks across the globe.
With all of the excitement, announcements, and stellar talks going on at AGBT, we couldn’t capture it all. Let us know your favorite moments, tell us if we missed anything, and share your thoughts about the meeting below.
Illumina
Illumina’s most anticipated talk clarified their new long-read sequencing methodology known as Illumina Complete Long Reads (CLR). Many customers were unaware if this new technology would require modifications to existing instruments or if the method involved synthetic long reads.
The company’s presentation showed that the CLR process begins with the tagmentation of the DNA, which normalizes the long fragment sizes. These fragments are landmarked to capture single molecule, long read information, and then the molecules are amplified. Long fragments containing the landmarks are then tagmented again to become the standard size for short-read sequencing libraries. After sequencing, the landmarked regions are used to assemble the long reads. An image of the process from Illumina’s CTO can be seen here.
Much of Illumina’s main efforts during the meeting were centered on promoting the success of their newest pair of sequencers: NovaSeq X and X Plus. After announcing the release of the instruments last September, they successfully shipped their first sequencer to the Broad Institute. Illumina officials and star customers presented data comparing the results against the older NovaSeq 6000. Key metrics like consistently high Q-values throughout the entirety of the run were shown to highlight the improvements.
Final presentations from Illumina explained the upgrades and performance of their popular NextSeq 2000. The new chemistry, XLEAP-SBS, will be available later this year with their designated P4 flow cell, while compatibility with other flow cells and kits will be accessible in the future.
Bio-Rad Laboratories
Bio-Rad presented results during the meeting highlighting updates to their SEQuoia RNA Sequencing Library Preparations. Collaborating with Singular Genomics and Element Biosciences, the popular kits are now compatible with their respective G4 and AVITI sequencers. This update was part of the company’s concerted efforts to make these high-performance kits accessible to users regardless of the platform. Bio-Rad also showcased the SEQuoia Complete Kit’s ability to perform comprehensive transcriptome profiling of low-quality FFPE samples.
Another important announcement for Bio-Rad was the release of their QX600 Droplet Digital PCR System, which was designed for quantifying multiple targets with enhanced accuracy, reproducibility, and sensitivity. The company displayed the QX600 System alongside their CFX Opus Deepwell Real-Time PCR System for conference attendees.
Element Biosciences
Talks from Element Biosciences emphasized the updates and direct applications of their AVITI sequencing platform. Since their first shipment of AVITI in May of 2022, Element has provided many upgrades to their instrument with hints of more big updates in the future.
Matthew Kellinger, VP of Biochemistry and Co-Founder, gave details about Element’s new Cloudbreak chemistry. With an expected release in April, Cloudbreak significantly reduces sequencing times while increasing accuracy. The cost of sequencing with this new chemistry is an estimated $200 a genome, or $2 per gigabase.
During the meeting, Element also introduced the Elembio Cloud Platform (ECP). This software portal allows users to configure and manage their instruments and user access, as well as
monitor their sequencing runs remotely.
Several other presentations covered the direct benefits of avidity sequencing and the application of the technology in single-cell research, cancer genomics, and metagenomic analysis. Direct comparisons against competitors’ instruments supported Element’s message of lower costs with high-accuracy sequencing.
10x Genomics
10x Genomics, single-cell sequencing and spatial biology provider, showcased several unique instruments. Their new Chromium Flex was shown to provide quality data with samples that are fresh, frozen, and FFPE tissue. The increased scalability of the Flex allows users to process millions of cells and hundreds of samples in a single experimental run.
Their Visium CytAssist instrument, which simplifies their Visium spatial discovery platform, was presented to include more advantages and capabilities. The device will have increased compatibility with different sample types and doesn’t require tissue optimization. In addition, 10x Genomics is preparing to launch the ability to co-detect protein expression and genes from the same FFPE tissue section. Data from the new Visium HD showed whole transcriptome discovery from whole tissue sections at single-cell scale resolution.
Updates to the Xenium In Situ platform were also covered at the meeting. The company provided a roadmap that demonstrates the future directions for the platform. This roadmap includes a 5,000 plex multi-tissue gene panel on seven human FFPE tissues, multimodal cell boundary stains with a trained cell segmentation algorithm, multiplexed RNA and protein on the same section, and isoform mapping and SNV detection.
Spatial Biology
The continued expansion and popularity of spatial biology products was evident at the conference. Vizgen, Akoya Biosciences, NanoString, and 10x Genomics all presented their instruments along with their unique aspects.
NanoString stood out as the Gold Sponsor for the meeting, and their GeoMx and CosMx platforms exhibited their multiplexing abilities.
The MERSCOPE from Vizgen was demonstrated to perform high-quality data and the simultaneous detection of RNA and proteins.
Akoya Biosciences’ PhenoCycler-Fusion also showed multi-omic (protein and RNA) work in addition to clinical applications.
Finally, 10x Genomics presented their new directions with Xenium in their roadmap as previously mentioned.
Individual Presentations
Last but certainly not least, AGBT was packed with talks covering the extraordinary work being done across the field of genomics. Below are only a few of the notable talks given.
• Karen Miga focused on her efforts with long-read sequencers and their ability to push the limits of complete, accurate genome assemblies. The data presented showed the results from her trials with PacBio’s HiFi and Oxford Nanopore Technologies’ (ONT) duplex reads. Slides for her talk were kindly uploaded here.
• Heonseok Kim demonstrated a multiplex CRISPR editor with an ONT long-read sequencing method. This allowed for gene expression and variation detection within the same cells to examine variants of unknown significance.
• Beth Shapiro gave a talk on her genetic studies of bison, past and present, along with the interesting history of ranchers interbreeding cow and bison to produce beefalo.
• Chris Mason spoke about his team’s work on the Spatial Atlas of Human Anatomy (SAHA) Project. This is a collaboration between NanoString Technologies and Weill Cornell Medicine to create a high-content spatial map of the human body.
• Alex Cagan presented his work on somatic evolution across the tree of life. He explained how spontaneous deamination, endogenous errors, and reactive oxygen damage lead to somatic mutations in mammals.
• Pardis Sabeti talked about her work on Sentinel (a pandemic preemption system) and covered her experiences monitoring deadly outbreaks across the globe.
With all of the excitement, announcements, and stellar talks going on at AGBT, we couldn’t capture it all. Let us know your favorite moments, tell us if we missed anything, and share your thoughts about the meeting below.