NEW YORK – A pair of new sequencing reagent kits from Illumina launched this week should provide big savings to certain customers and help make it more efficient to run counting applications on the firm's most powerful platform, the NovaSeq X.
Earlier this week, Illumina announced the availability of the 25B 100-cycle and 200-cycle next-generation sequencing kits, intended for such uses such as single-cell gene expression profiling that analyze shorter molecules than other applications that are better served by the existing 300-cycle sequencing kits. The new 100-cycle kit has a list price of $11,700, and the 200-cycle kit costs $14,500.
Now, customers running very large single-cell sequencing projects can access the NovaSeq X instrument's highest levels of throughput. Illumina's 25B kits are specified to produce at least 26 billion reads per 25B flow cell. Previously, 100- and 200-cycle kits were only available for Illumina's 10B flow cell. Alternatively, customers could use the more expensive 25B 300-cycle kits, which have a list price of $16,000.
"Anybody that doesn't need a [paired-end 150 bp read] is going to benefit from this," said Eric Chow, a core lab director at the University of California, San Francisco. In addition to single-cell RNA-seq, single-cell ATAC-seq and NGS-based proteomics such as the Olink assay could be run using the kit. Customers with enough samples will also benefit from moving up from the 10B 100-cycle kit to the 25B kit. "It's cheaper and you get more data," he said.
Moreover, the kit can help core labs like his make better use of their sequencers. "It's going to help us squeeze more runs out of the machines," Chow said. "It's a much more efficient use of capital equipment." In addition, a concurrent software release could mean even more total output, he said.
"Customers have asked for these kits since we launched NovaSeq X, and we are excited to deliver on their requests," an Illumina spokesperson said in an email. The kits began shipping in December and are compatible with the PipSeq single-cell transcriptomics method acquired through last year's purchase of Fluent BioSciences, now rebranded as Illumina Single-Cell Prep. Illumina also announced the availability of a single-flow cell NovaSeq X instrument and a new software upgrade for the instrument line this week.
The new kits bring Illumina's highest levels of throughput directly to the single-cell sequencing field. Startup competitors Element Biosciences and Singular Genomics Systems also offer sequencing kits for these kinds of applications for their mid-throughput, benchtop instruments. The 100-cycle kit may also narrow the price gap per read with Ultima Genomics, which has targeted sequencing-intensive applications like single-cell transcriptomics as a market for its UG 100 instrument.
Element launched a 2x75 bp paired-end sequencing kit in 2022 and updated it with its Cloudbreak chemistry to run 1 billion reads in 20 hours. Singular, which has since shifted focus from NGS to spatial multiomics, launched its Max Read reagents in early 2023, offering 800 million reads of approximately 30 bp to 100 bp per flow cell.
For core labs with the NovaSeq X Plus, which runs two flow cells, the new kit can offer operational benefits. "I think it will slightly increase our throughput," said Claire Hartmann, director of the Bauer Core at Harvard University. She noted that her lab has mostly used the 25B 300-cycle kit for single-cell sequencing jobs for the purpose of maximizing throughput and turnaround time.
Chow noted that his lab has already run approximately 10 runs using the new kit. "They're pretty popular," he said, especially for 10x Genomics' single-cell gene expression assays, as studies with more cells need more sequencing. "Assuming people want about 25,000 reads per cell, that's maybe 100,000 cells," he noted.
"For every 16 lanes of a 10B flow cell, you only need to run eight lanes with the 25B kit," he said. "Both runs take a day. This gives us more than double the throughput."
He noted that the software update has added marginal but very real gains in total reads coming off the instrument. The number of reads passing filter, a run quality metric, has been "a couple percent higher" with the new software, he said. That means they're now getting approximately 33 billion reads per flow cell, well above Illumina's stated specs, up from around 30 billion to 32 billion reads.