By Kevin Davies
October 12, 2011 | MONTREAL – Illumina’s much anticipated benchtop next-generation sequencing (NGS) instrument, the MiSeq, enters full production with a series of enhancements including streamlined sample processing and a new Cloud platform called BaseSpace that supports the platform.
“We’re changing what people need,” says Illumina’s Jordan Stockton, associate director for product marketing, computational biology.
The goal of the new BaseSpace Cloud platform, says Stockton, is “to provide a seamless pathway to get data there, expand on the space, and provide different types of analysis tools. We’re really excited about the Cloud. It’s a canned workflow and solves the storage and collaboration problem in one swing.”
“The addition of BaseSpace eliminates the need for expensive IT infrastructure, simplifying the process of adopting a personal sequencer for labs of any size and experience,” commented Illumina CEO Jay Flatley.
“We want to push people to the Cloud because we think it will be an easier, most affordable [solution] and provide a higher level of collaboration. But you can take the bases and qualities of the sequenced DNA and move them anywhere you want,” says Stockton.
The Cloud platform is deployed using Amazon EC2. “They’ve really helped us get things deployed robustly,” says Stockton. In the future, BaseSpace will be compatible with the HiSeq 2000 as well, becoming a general purpose tool for base level data, but it is currently limited to the MiSeq.
Illumina says it will offer customers and non-customers access to Base Space at launch, allowing them to examine data shared publicly. “Anyone can go and have a deep look at the data,” says Stockton.
After shipping about 45 MiSeq instruments in the third quarter of 2011, Illumina says it is now in full-scale production, with a healthy backlog. The MiSeq, which retails for $125,000, is expected to enjoy healthy competition with the Ion Torrent Personal Genome Machine for the benchtop NGS market.
A strong testimonial comes from Elaine Mardis, co-director of The Genome Institute at Washington University. “The MiSeq was by far the best 'plug and play' instrument we've tested in over 20 years of instrumentation evaluation,” says Mardis. “Within a week, we went from crate to installation and generated four runs with high data quality -- paired 150-basepair reads… The high-quality, one-day turnaround will facilitate our applications development and bring next-generation sequencing one step closer to the clinic.”
Stockton says Illumina has built a markedly streamlined NGS workflow compared to a year or so ago, when researches doing targeted sequencing would have to prepare amplicons, figure out the reagents, perform simulations, order (or synthesize) probes, perform DNA enrichment and purification, build libraries, and multiplex, all before setting up a sequencing run and then demultiplexing.
“We’ve boiled this down,” says Stockton. “Now you can design probes online… and plug in the enriched sample. You press ‘Go’ on the MiSeq after loading the cassette, and in real time, data are processed to bases, and sent to the Cloud for archival storage.”
“This changes the look and feel of doing targeted resequencing,” says Stockton.
The MiSeq runtime is 27 hours for a 2x150-basepair run, for a total throughput of 1.7 Gigabases. The shorter runtime allows researchers “to keep the chemistry more precise over the course of the run, largely because of the shorter time that reagents sit in the cavity of the flow cell,” explains Stockton.
The longer read-length is brought about by numerous factors: reductions in the chemistry time, incubation time, and scanning. Microbial sequencing will be an attractive niche, where turnaround times can be reduced to under a day, with an improved 90-minute sample prep for genomic DNA. “You can go from sample to results overnight,” says Stockton.
In addition, the MiSeq has several workflows wrapped into the onboard computer, so it will deliver variants for applications including phylogenies for metagenomics to de novo assembly, on the instrument.