New Technologies

Revio: Newest generation long read sequencer from PacBio

• Upgraded flow cells with 25M ZMWs (3x increase from Sequel IIe)
• Shorter runtimes/parallel sequencing
• On-board computation with Google DeepConsensus (>20x more computing power)

NovaSeq X Plus from Illumina

• XLEAP-SBS chemistry – an even faster, higher quality, and more robust version of sequencing by synthesis (SBS) chemistry.
• Ultra-high density patterned flow cell
• Three flow cell types (1.5B, 10B and 25B) and up to 16Tb output per run (~ 3 times increase from current NovaSeq 6000)

Nabsys: High-Definition Mapping (HDM) using electronic detection of tagged single high molecular weight (HMW) DNA molecules

• HDM provides routine, accurate, cost-effective analysis of genomic structural information, unavailable with short read technologies.
• These characteristics make HDM an ideal first-line approach for a variety of applications for small and large genomes, including de novo map assembly, structural variant analysis, hybrid assembly, metagenome characterization and strain identification.

Xdrop-Sort: Target DNA enrichment for SV or virus integration detection

• A novel microfluidic-based system that allows for targeted enrichment of long DNA molecules using only a few nanograms of DNA.
• Based on the isolation of long DNA fragments in millions of droplets, where the droplets containing a target sequence of interest are fluorescently labeled and sorted. The final product is an enriched population of DNA molecules that can be investigated by long read sequencing.
• Single cell RNA-seq applications will be coming soon with the release of a new cartridge from Samplix.

Oxford Nanopore, Direct Protein Sequencing:: The Sequencing Facility, in collaboration with other proteomics labs within CCR, such as the Protein Characterization Laboratory and the Protein Expression Laboratory, is highly interested in acquiring and developing new emerging technology from Oxford Nanopore Technologies. This innovative technology enables the reading of amino acid sequences for specific proteins by detecting changes in ionic current as the amino acids pass through a nanopore.

Single-cell Spatial Proteomic: The Pixelgen single-cell spatial proteomic technology using for cell surface protein-protein interaction and colocalization studies. This technology uses barcoded antibodies to bind multiple proteins and ligate the neighboring barcodes together to detect protein colocalization. We can collaborate with the CCR Protein Characterization Laboratory (PCL) within the LBR to validate this technology.

Illumina Direct Base Modification & Comprehensive WGS: One of the new applications Illumina is developing is the 5-base genome, which will enable both genetic variant and methylation detection in a single whole genome assay. This approach allows for direct interrogation of methylation without the cumbersome bisulfite conversion process. Another innovative product from Illumina is the comprehensive Whole Genome Sequencing (WGS) solution, designed to perform library preparation directly on the flow cell. This product provides comprehensive insights, including single nucleotide variants, structural variants, phasing, and repeat expansions. By eliminating traditional library preparation steps, this technology reduces labor, shortens turnaround times, and minimizes variability and failure points.

Chromatin Conformation Capture, Pore-C: Pore-C is an end-to-end workflow that combines 3C with long nanopore sequencing reads, offering contact information that enables existing assemblies to be scaffolded with high contiguity. Unlike traditional 3C methods, which typically detect pairwise interactions between two genomic loci, Pore-C generates higher-order contact information from multiple loci. The method is amplification-free, allowing access to GC-rich and repetitive genomic regions. Additionally, epigenetic modifications are preserved in the long nanopore reads and can be characterized alongside the nucleotide sequence.