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Illumina predicts expansion of both small- and large-scale sequencing

San Diego’s Illumina made headlines in January when the company said it “broke the sound barrier” of genomics by facilitating the sequencing of the human genome for a mere $1,000 using the company’s HiSeq X Ten System of machines.

Illumina (Nasdaq: ILMN) has long been at the forefront of genomics, having entered the field in 1998 with genetic analysis products and then turning to genetic sequencing when it acquired Solexa Inc. in 2006. Since then it has compiled an array of products ranging from something suitable for an individual principal investigator through factory-like production centers studying entire populations.

Joel Fellis, Ph.D, senior manager of product marketing, systems and genomic services at Illumina, said instead of a convergence around one end of that spectrum, Illumina is excited about an expected increase in opportunities on both the smaller and larger side.

“It’s going to be a combination of the two,” Fellis said. “Really, there’s an insatiable appetite for sequencing data; a platform like NextSeq enables individual researchers to take on projects different than those at large human genome facilities. These large centers processing tens or hundreds of thousands of genomes deliver a tremendous amount of genetic information, and fuel individual researchers doing research on NextSeq. Their databases allow other labs to do follow-up studies, going deeper into the functional biology underneath that. So it has to be a combination of the two.”

Among Illumina’s current sequencing offerings are the MiSeq, NextSeq and HiSeq2500 and HiSeqX Ten platforms, some of which have derivations within each platform. In terms of complexity and scale of use, Fellis said the MiSeq systems are on the lower end.

“That’s really a desktop sequencer,” he said. “Typically used in smaller labs and by individual professors and researchers, it has lower throughput applications that don’t require a massive amount of data.”

Fellis said the MiSeq platform is particularly useful for studying gene panels or sequencing microbes.

The next step up is the NextSeq500, which also is a desktop system for smaller labs or individual use, and was announced in January. The main difference between this system and the MiSeq platform is that it can accommodate high-throughput sequencing, which requires more data. Fellis said it’s possible to use the NextSeq500 to do the same studies as on the MiSeq, but on a larger scale. In addition, it can accommodate the large amount of data needed to sequence entire human genomes, though it can only handle one at a time. Fellis said it’s the only desktop sequencer available that can facilitate this.

The NextSeq500 works well for transcription sequencing, profiling RNA transcripts, and exome sequencing, and has two run modes depending on the amount of samples being run.

The HiSeq2500 platform offers flexibility in the ability of data to be processed, and is particularly notable because it can sequence an entire human genome in 27 hours, or roughly one day.

“It was the first platform in the world capable of sequencing the human genome at that speed,” Fellis said.

This system is often used by labs or groups looking to process large samples, since the high output mode has higher throughout applications that can sequence 10 human genomes in six to seven days, churning through hundreds to thousands of samples annually.

“It also does exome transcription sequencing, but the difference is it can process many more samples in a run,” Fellis said. “Hiseq is better suited for thousands of samples -- an order of magnitude more samples than the NextSeq, which is the difference between a desktop sequencer versus a production sequencer.”

Illumina’s final sequencing platform is the HiSeqX Ten, announced in January alongside the NextSeq500. The system is actually a package of 10 machines sold together for $10 million, with each of the 10 systems capable of sequencing a human genome for $1,000.

“That’s just changed the world of genomics and is a huge milestone for the community,” Fellis said. “It has an incredibly high throughput designed for population scale sequencing of the human genome.”

He said the 10 machines used together can sequence 18,000 genomes per year, and the system has created a tipping point in the industry where huge factory-scale sequencing of the human genome is now possible and being increasingly used.

Fellis said while he couldn’t comment on specific new products Illumina is working on, he said the next milestone after breaking the “sound barrier” of the $1,000 genome is in enabling population-scale projects.

“One thing I can answer is that the next big milestone is enabling population-scale projects,” Fellis said. “We’ve enabled the price-point, throughput and now I think we’re ready to see large centers take on projects and sequence large populations, which is good for the entire genomics community.”

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