DeciBio Insights

Illumina launches the NextSeq 500 and HiSeq X Ten

Clinical Diagnostics, Research Tools

San Francisco, CA – January 14th, 2014 – Illumina announced today at the JP Morgan Healthcare conference that it has launched two new sequencing platforms: the NextSeq 500 (available now) and HiSeq X Ten (available in Q1 2014). At a high level, the NextSeq 500 seemed positioned to compete with the Ion Proton, while the X Ten essentially corners the ultra-high throughput market.

NextSeq 500
The NextSeq 500 system is a system that we predicted would be launched by Illumina in our NGS report back in March 2013, based on two observations: 1) the ability of Illumina to offer a $125,000 upgrade to HiSeq 2000 customers to transform their instrument into a HiSeq 2500; 2) a clear need from interviewed customers for an instrument in the 100 Gb-throughput segment to conduct a broad range of key applications (e.g., exome sequencing, whole transcriptome sequencing.

“… A competitive response from Illumina [to Ion Torrent’s P2 chip] is expected in the near future to fill the gap that currently exists between its low throughput MiSeq (~10 Gb) and high throughput HiSeq 2000 (~600 Gb). The current HiSeq 2500 does not adequately address the mid-throughput space, as the instrument remains prohibitively expensive (~$700K).” (NGS report, March 2013)

“…Illumina’s competitive response to Ion Proton (P II and P III) [is expected to] be a lower cost workhorse instrument. This expectation is grounded in the fact that Illumina currently offers its 2500 upgrade for ~$125,000, suggesting that they plan to develop a lower cost next-generation workhorse instrument. At 50 – 200 Gb throughput, this instrument will sit at a sweet spot for a number of key applications, such as WES and whole transcriptome analysis …” (NGS report, March 2013)

The $250,000 desktop system that has two run modes: a mid-output mode that generates ~40 Gb per run and a high-output mode that generates ~120 Gb per run. As a result, this platform actually has the capability to sequence one entire human genome in a single run, a first for a desktop sequencer. The platform integrates cluster generation and sequencing into a single instrument, simplifying workflow. The NextSeq generate data in <12 hr (75 bp sequencing) and <30 hr (paired 150 bp sequencing). Reagent kits are expected to cost between $1,000 and $4,000.

As stated by the company: “The NextSeq 500 System delivers the power of high-throughput sequencing with the load-and-go simplicity of a desktop sequencer, effectively transforming a broad range of high-throughput applications into affordable, everyday research tools. Its push-button operation delivers a one-day turnaround for a number of popular sequencing applications, including one whole human genome and up to 16 exomes, up to 20 non-invasive prenatal testing samples, up to 20 transcriptomes, up to 48 gene expression samples and up to 96 targeted panels.”

The inital response from scientists we talked to appear positive. Ken Baughman, a scientist at the Okinawa Institute of Science and Technology (OIST) told us in an email: “As a basic researcher working on marine genomics, I have been really impressed with the MiSeq platform. It feels like NextSeq is more of the same, and may be particularly useful for transcriptome work […] Kit cost is a real factor, and it often feels like bioinformatics is a bit of a bottleneck. That said, NextSeq should seamlessly fit into my current pipelines, with economics that are going in the right direction. I don’t think the NextSeq will fundamentally change what I currently study, but I can see how it will make my research better.”

We look forward to Ion Torrent’s response in the coming months, perhaps at AGBT.

HiSeq X Ten
HiSeq X Ten is an ultra-high throughput platform, and the world’s first system to deliver full coverage human genomes <$1,000 (at the standard 30x depth). Remarkably, this price tag include instrument depreciation, DNA extraction, library preparation, and estimated labor. One reagent kit is expected to enable sequencing of 16 genomes per run and cost $12,700 (just shy of $800 per genome); on top of that, hardware is expected to add $140 per genome, and sample prep ~$60 per genome. We confirmed that the math checks out if the instruments are run at full capacity (~18K genome per year).

The HiSeq X Ten platform is composed of 10 HiSeq X Systems. While the platform has been built for the purpose of human whole genome sequencing (WGS), other applications may follow (e.g., whole exome sequencing), as this current limitation is due to software (as opposed to more problematic hardware) restrictions. Each platform is expected to generate 1.8 Tb of sequencing data in <3 days. The system is expected to cost $10M ($1M per instrument).

Initial customers include Macrogen, a global next-generation sequencing service company (Seoul, South Korea), the Broad Institute (Cambridge, Massachusetts), and the Garvan Institute of Medical Research (Sydney, Australia). The Garvan institute intends to use the system to accelerate the introduction of clinical genomics and NGS-based clinical medicine in Australia.

As the HiSeq X Ten can sequence ~18,000 genomes annually, one important question remains whether the market is ready to absorb such large capacity. In the past, Illumina has released kits that generated capacity that the market took time to absorb. Regardless, this platform along with the other HiSeq franchise consolidates Illumina’s position at the high-throughput end of the NGS market.

Of note, this platform will directly compete with Complete Genomics’ services. Recently, at ICG8, the company announced a 30X increase in throughput of its instrument.

Authors: Stephane Budel, Partner at DeciBio, LLC

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