Last week at the J.P. Morgan Healthcare Conference, Illumina presented their new sequencers, the NextSeq 1000 and NextSeq 2000. 

Strengths: The NextSeq 1000 and 2000 use patterned flow cells similar to the NovaSeq 6000 System that offer the highest cluster density flow cell of any on-market NGS system. To take full advantage of these higher density flow cells, they feature a novel super resolution optics system that is optimized to increase cluster brightness, reduce channel cross-talk, and improve signal-to-noise ratio. This should increase the output and reduce the cost per run compared to the previous NextSeq model (1). The system uses fluors, which both excite and emit with blue and green wavelengths. 

The major difference between the NextSeq 1000 and 2000 capacities is that only the 2000 will be able to handle the larger P3 flowcell. To compare the P2 and P3 flowcells at the 2×150 read length, the P2 flowcell will yield a similar number of clusters to the NextSeq 550 Hi Ouptut kit for a similar runtime. The P3 flowcell will yield a number of clusters that is between the NovaSeq’s SP and S1 flowcells, although the run time is longer, which is likely due to the new super resolution technology. According to Illumina, the NextSeq 2000 will have a $20 per Gb cost, and the NextSeq 1000 will have a $30 per Gb cost (2). 

Regarding downstream data analysis, these new sequencers also come with the DRAGEN system, which is both on-board and cloud-based. The DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform will enable our providers to automate a variety of genomic analysis, including BCL conversion, mapping, alignment, sorting, duplicate marking, and variant calling. According to Illumina, results can be generated in as little as 2 hours (1).

On the wet bench side of things, the NextSeq 1000 and 2000 reagents will also reduce the volume of the sequencing reactions. This volume reduction should decrease waste and minimize physical storage requirements. For example, one cartridge includes all reagents, fluidics and the waste holder (1), which will simplify library loading and instrument use. This should increase efficiency, reduce the chance of user error, lower the sequencing costs, improve recyclability and minimize waste volume. Ideally, these cost savings will then be passed on to our clients. 

Applications: According to Illumina, the new applications available on the NextSeq 1000 and 2000 are small whole-genome sequencing, whole exome sequencing and single-cell RNA-Seq (1), applications which are useful for research in oncology, genetic disease, reproductive health, agrigenomics, etc. 

As some analysis examples, the new DRAGEN Enrichment Pipeline can be applied to whole exome sequencing and targeted resequencing with alignment, small variant calling, somatic variant calling, SV/CNV calling and custom manifest files. The DRAGEN RNA Pipeline can be applied to whole transcriptome gene expression and gene fusion detection with alignment, fusion detection and gene expression. Other standardized DRAGEN pipelines include DRAGEN-GATK, DNA/RNA targeted panels and single-cell sequencing. A more complete list is available here.

Release Date: The NextSeq 2000 is available for order now, but both the NextSeq 2000 and 1000 will only be available for shipment in Q4 2020. The NextSeq 1000 has a list price of $210,000 and the NextSeq 2000 has a list price of $335,000 (2). We have already added the instrument specifications to our database, so providers can start listing their NextSeq 1000 and 2000 services as soon as they are ready.  

Overall, the new NextSeq 1000 and 2000 seem like solid desktop upgrades and also good testing ground for the new super resolution technology. If it goes well, there may be an upgraded version of the NovaSeq unveiling in the future.