Illumina Launches New MiSeq i100 Series with XLEAP Chemistry, RT Reagents

By Julianna LeMieux, PhD

Credit: Illumina

Weeks of teasers on social media noting that “Something big is coming. And it’s small,” have sparked a guessing game (and some patent searching) among NGS aficionados. But today, Illumina quelled the rumors with the launch of an updated MiSeq series of sequencing systems: two new instruments, MiSeq i100 and MiSeq i100 Plus. The MiSeq is a benchtop sequencer, first launched in 2011, designed for smaller, quicker, sequencing needs.

The new MiSeq i100 series instruments have incorporated ­­XLEAP-SBS chemistry (once dubbed Chemistry X) first debuted two years ago with the launch of Illumina’s NovaSeqX instrument. In addition, the new MiSeq i100 series has DRAGEN (Illumina’s data analysis tool) integrated on-board. Another advance that the company is emphasizing is room-temperature storage and shipping for reagents.

The last time Illumina launched a sequencer, the NovaSeqX, was in the fall of 2022. The launch was a large-scale production, with an in-person event in San Diego—the Illumina Genomics Forum—that hosted multiple big name speakers including a headline interview with former President Barack Obama.

But the MiSeq i100 launch today was done via a webinar. (And unless Obama was in the chat, it was devoid of former Presidents.) Why? “I think it’s redefining how we launch products,” said Joel Fellis, PhD, vp of global product management at Illumina. “We want to launch to our customers with our customers. We’ve had some [MiSeq i100] users and they will be front and center in the webinar. We are getting back to basics and making customers the hero.”

The new MiSeq i100 comes in two configurations: the MiSeq i100 System and the MiSeq i100 Plus System. The difference lies in the number of reads per run, and cost.

There are four flow cell options ranging from five million single-end reads up to 100 million single-end reads (but each instrument runs only one flow cell at a time.) The MiSeq i100 System runs flow cells that provide 5M or 25M reads. And the MiSeq i100 Plus System can run those, and also flow cells that run 50M and 100M reads. The MiSeq i100 System costs just over $49,000 and the MiSeq i100 Plus system costs just over $109,000.

The speed depends on the flow cell being used, with run times less than four hours for certain use cases. Illumina noted that all flow cells can run 2×150 in under eight hours and 2×300 take about 15 hours on 5, 25, and 50M read flow cells.

There is not a diagnostic version of the new MiSeq i100 at the moment, and the company does not have a timeline for one. But they are in active discussion about further development.

When asked when the last update to MiSeq was announced, Fellis thought for a moment, and couldn’t quite remember. But that is not to say that innovations haven’t been made in the Illumina benchtop space. There have been line extensions to the MiSeq along the way: the introduction of new kits, and new flow cells that provide more reads and read length. In addition, the FDA granted Illumina premarket clearance for Illumina’s MiSeqDx system, the first high throughput DNA sequencing analyzer to receive such approval, in November 2013.

In addition, two smaller instruments have been launched since the 2011 launch of MiSeq: the Miniseq (a lower output benchtop instrument than the MiSeq) was launched in 2015 and the most recent benchtop platform–the iSeq—with even lower output, was launched in 2018.

So, it was about time for an update. The project was started about three years ago—in the middle of the COVID-19 pandemic—not long after the launch of the iSeq. The timing, and the events going on, were influential, noted Fellis. There were many microbiology applications coming into the spotlight, and an increased focus on run time and turnaround time.

Who is the target user of the MiSeq i100? The company envisions that new PIs will adopt MiSeq i100. Fellis predicts that “more and more, NGS is going to be standard lab equipment, even common in most molecular biology labs.” Areas where MiSeq i100 could make an impact are researchers in pathogen detection, analyzing genomic variations in tumors, and researching antimicrobial resistance.

And, for the first time, Illumina is offering a menu of applications (18 end-to-end workflows across 10 applications) directly on the instrument. Some are listed below.* Illumina noted that ease of use has been built out in much greater detail on day one. In contrast, for NextSeq and other platforms, users had to build these workflows out on their own. And the validated workflows are, noted Emmanuel Naouri, product management, NGS systems lead, Illumina, catered to the particular customers listed above that they think will adopt the new systems.

“Our customers told us they need a faster, smaller, and easy-to-use instrument, and that’s what we’re delivering with the MiSeq i100,” said Jacob Thaysen, PhD, CEO of Illumina.

When asked what’s next at Illumina, Fellis said that the company is “focused on innovation to meet our customers. We have spent the last three years innovating to meet use cases where it wasn’t met.” The future, he said, will bring more assays, particularly multi-omic assays, and software capabilities along with the continued evolution of their platforms.

In the near future, Illumina will be out on the road with the MiSeq i100. They are eager to showcase the new instrument at upcoming conferences, including ASHG next month. The company will also not only be at AGBT in Florida next February, but it is the gold sponsor. When asked why they wanted top sponsorship this year, Fellis responded, “Our CEO, Jacob Thaysen, laid out a new corporate strategy in August, and our commitment to customers is central to that vision. As Illumina continues to deliver the most crucial innovation driving genomic discovery, our presence at scientific meetings will create important opportunities to engage with our customers, feed our innovation engine, and showcase solutions that meet our customers’ needs.”

* Applications