Oxford Nanopore Launches Epic Sequencer, 10x Genomics Partnership

By Bio-IT World Staff 

November 1, 2022 | It’s been a big month for sequencing news, and Oxford Nanopore with 10X Genomics joined PacBio and Illumina in making new announcements.  

Last Monday, Oxford Nanopore announced the PromethION 2 (“P2”) Solo sequencer, a small, portable, high-yield platform equivalent in size to one printed volume of the Lord of the Rings trilogy, according to the company. 

The P2 Solo combines the latest R10.4.1 flow cells with the latest Kit 14 to deliver sequencing data that achieves modal raw-read simplex accuracies of 99.6% (Q24) and single molecule duplex accuracies of 99.92% (Q31) with tunable run conditions for further flexibility and optimization. The P2 Solo can use any-length native reads (from 20 bases to more than 4 million bases) and captures full biology including SNPs, INDELs, structural variants and methylation from a single flow cell. The company boasts that one to two genomes can be processed per flow cell. 

The P2 Solo starter pack is priced at $10,455, using Oxford Nanopore’s “box-is-free” model. Users will be able to comprehensively sequence as many as 190-380 human genomes per year on the P2 Solo, and scale to ~ 4,600-9,200 human genomes per year with the PromethION 48 (“P48”). That comes to less than $1,000 per genome with the P2 Solo, the company says. When running in production mode with P48 devices, the company expects genome prices of approximately $300 to $600 (at 1-2 human genomes per flow cell, simple library prep costs from $43 per genome, with no additional cost for device, methylation and any-length fragments) with a future pathway for further reductions. 

The release of P2 Solo is accompanied by a whole genome workflow in EPI2ME, Oxford Nanopore’s data analysis solution, enabling users to simply upload their files and receive small variant, structural variant and methylation reports back with a simple click. 

The PromethION 2, Oxford Nanopore’s fully plug and play benchtop nanopore sequencer in the same range as the P2 Solo, contains a powerful GPU and runs two high-yield PromethION Flow Cells. This is available for pre-order and will be available for shipment in the coming months. 

Single Read Partnership 

Later in the week at the American Society of Human Genetics meeting, Oxford Nanopore and 10x Genomics announced a collaboration to enable a streamlined workflow for sequencing full-length transcripts in single reads on highly accessible Oxford Nanopore devices. The goal is to enable users to span features such as fusion genes or transcripts with repetitive regions, producing abundant, cost-effective single-cell and spatial sequencing data.  

The collaboration covers the addition of Oxford Nanopore’s PromethION devices and selected consumables, in conjunction with sample preparation on the 10x Genomics devices, into the 10x Genomics Compatible Partner Program (CPP). Alongside this, Oxford Nanopore has also released a new openly available end-to-end nanopore-only single-cell protocol. Both parties believe this will enable a streamlined customer experience and highlight the compelling utility of nanopore-based sequencing in conjunction with 10x Genomics workflows.   

The analysis of genomic and transcriptomic heterogeneity at the single-cell level has provided new insights into many research areas, including cancer research, cell biology, embryonic development and immunology. However, Oxford Nanopore said in a release, the use of traditional short-read sequencing technology can leave certain types of information like isoform-specific transcript abundance invisible to researchers. Additionally, the 10x Genomics App Note outlines how data on cell calling and clustering from sequencing long fragments is comparable to short reads and, upon further analysis of data from sequencing long fragments, it was possible to accurately identify isoforms differentially expressed between cell types.  

Nanopore sequencing reads resolve these challenges, enabling end-to-end sequencing of full-length transcripts in single reads, which span features such as fusion genes or transcripts with repetitive regions. By combining the power of 10x Genomics’ single-cell and spatial assays with nanopore sequencing, researchers have a powerful new tool to see unique differences in isoform expression, alternative splicing, cellular sub-types, immune receptor profiling, spatial transcriptomics, and other emerging applications.