Next-generation sequencing (NGS) has moved away from expensive runs and complicated workflows into a new era where benchtop instruments prioritize sustainability, accessibility, accuracy, and speed. In this Innovation Spotlight, Emmanuel Naouri, associate director of Product Management, NGS Benchtop Systems at Illumina, discusses how the MiSeq i100 Series of sequencers was designed to meet the needs of experienced NGS users while offering the simplicity and support necessary for researchers new to the technique.
Emmanuel Naouri
Associate Director
Product Management, NGS Benchtop Systems
Illumina
Illumina
What are some of the perceived barriers to entry when it comes to NGS?
The perceived barriers to entry for NGS include the need for NGS expertise in the lab, including experts in genomic sequencing and bioinformatics. Cost of the instrument as well as total cost of ownership is another barrier for many labs wanting to add NGS capabilities.
To circumvent these barriers, our new instrument is designed for simplicity and ease of use from the moment it arrives in a lab. Initial setup does not require Illumina support, while lab technicians can be trained to run the instrument. We offer total workflow solutions to streamline operations through the entire sequencing process, from sample to analysis.
When it comes to cost, the MiSeq i100 Series comes in two configurations with different price points, providing affordable solutions to various types of customers. The flow cells for the MiSeq i100 support lower data output and sample throughputs, which is ideal for applications requiring a low number of samples and library quality control. The MiSeq i100 Plus System accesses a wider range of throughputs for more sequencing per sample and larger studies. Applications like small, targeted panels for oncology, infectiology, or microbiology are the perfect target for this solution.
Our focus on the value of the total workflow addresses each phase of the NGS process: library preparation, sequencing, and analysis. The ability to streamline this process from end-to-end facilitates cost and operational efficiencies for labs.
What needs do the MiSeq i100 Series sequencers fulfill?
The MiSeq i100 is ideal for customers who are new to NGS because it offers powerful insights through an affordable, comprehensive solution that is simple to understand and use, even for those with limited NGS expertise. With 18 pre-built, end-to-end, push-button workflows across 10 applications (and more coming in the pipeline), as well as same-day results, labs can get up and running quickly. Thanks to its simplicity and accessibility, groups that previously sent samples to a third-party lab for sequencing can now bring that NGS capability in-house.
For established NGS users, the instrument introduces capabilities to broaden into new NGS applications and the ability to sequence on-demand, with faster-than-ever run times, and cost effective, comprehensive workflow solutions that enable a new level of efficiency and productivity.
The MiSeq i100 overcomes the barriers to entry for many labs, and goes beyond to introduce, for the first time, extended room temperature storage for reagents, which unlocks on-demand sequencing and same day sample-to-analysis. Additionally, the instrument’s run time is four times faster than the original MiSeq, completing runs in as little as four hours. This creates meaningful impact for labs conducting work around infectious disease spread, pathogen monitoring, and analyzing genomic variations in tumors.
How will a benchtop sequencing instrument transform research?
Illumina’s MiSeq i100 sequencers come equipped with numerous pre-built workflows, giving researchers same-day results at the touch of a button.
Illumina
The speed and simplicity of MiSeq i100 enables labs to begin a run on-demand, thanks to no-thaw reagents, and to complete runs in the same day. Our early access customers have expressed their enthusiasm for how these features will enable them to do more and reach answers faster. Also, improved data quality allows scientists to publish with confidence.
MiSeq i100 will be used for a wide range of NGS research. For instance, as previously mentioned, this technology is ideal for identifying disease-causing pathogens, infectious disease monitoring, and analyzing genomic variations in tumors, in addition to researching drug resistance. Additionally, labs conducting exploratory research can rapidly test hypotheses with less time and cost invested.
What innovations or features were necessary to implement in the new sequencers to meet researchers’ needs?
We have incorporated the groundbreaking technology of our NovaSeq™ X system—extending the power of XLEAP-SBS™ chemistry, this instrument series enables faster sequencing and insights to more labs across the world. Additionally, the instrument facilitates data analysis in under two hours with included workflows and onboard or cloud-based DRAGEN™ genomic data analysis software.
Do the new sequencers incorporate any sustainability features?
The room-temperature storage and shipping feature gives customers even greater flexibility in how they plan and execute their projects, while reducing their environmental impact.
Ambient storage and no-thaw reagents reduces prep time, packaging, and storage space, helping labs respond faster to urgent samples with immediate run capability, and making sequencing more accessible to labs that do not have deep freezers or special storage equipment. Ambient storage also helps to improve the energy efficiency of our customers’ labs, in turn reducing their carbon impact and enabling them to progress forward against their sustainability targets.
Ambient shipping helps to reduce waste through the elimination of dry ice and ice packs, creating easier disposal for customers while reducing impact to the environment. Recyclable plastics and buffer cartridges simplify disposal for customers while reducing landfill waste. Overall, there is an 85 percent reduction in packaging materials compared to the original MiSeq System.
How do data quality and the analysis workflow compare to larger sequencers?
The performance of the MiSeq i100 Series matches or exceeds the data quality that benchtop customers have come to appreciate. The MiSeq i100 Series will have a minimum specification of greater than 90 percent of bases above a Q score of 30 (a measure of base calling accuracy), resulting in highly accurate (99.9 percent) data.
What advice do you have for scientists looking to perform NGS for the first time?
NGS has historically been very complex to perform, with complicated workflows that require specialized expertise. Building a bioinformatics pipeline demands very specific knowledge, and running an instrument requires intensive time and attention. With the MiSeq i100 Series, we are breaking down these barriers by simplifying the workflow and the analysis so sequencing can become as simple as qPCR. My advice is, don’t be afraid of sequencing anymore. Ask our teams how it can help generate more insightful information for your lab.
This interview has been condensed and edited for clarity.
