New, smaller sequencing instruments are finding niches everywhere. Earlier this year in Less Is More: Sequencing on the Benchtop, I profiled three pint-sized sequencing instruments designed for next-gen sequencing on the benchtop: IonTorrent’s PGM, the Illumina MiSeq, and 454’s GS Junior. I must admit that I’m most intrigued by the PGM, probably because the idea of semiconductor sequencing is just so fascinating.

One concern that I’ve heard about the PGM, however, was sample preparation. The time requirement and difficulty of sample prep was an immediate question at AGBT when Jonathan Rothberg first presented the instrument. He dodged the question, and I don’t think there’s been a satisfactory answer since. Until now. This morning, IonTorrent announced a new companion instrument, the Ion OneTouch System, that streamlines sample preparation for the PGM sequencer.

Priced at under $5,000, and measuring 1′ x 1′ square, the OneTouch requires “five minutes of hands-on time” and takes a few hours to run. It’s no longer the bottleneck, since the actual sequencing takes longer. The instrument is compatible with all three IonTorrent chips, which deliver throughputs ranging from 10 Mbp to 1 Gbp, with a single microgram of DNA.

PGM Applications

It’s a good thing to see the PGM constantly evolving – first the throughput was doubled, and now sample prep time cut substantially. At the price points we’re talking about, this might easily become standard equipment or small labs, academic departments, even single investigators. The current throughput of 1 Gbp isn’t enough for whole-genome or whole-exome sequencing, but it opens the door to a number of targeted applications. In Genome Technology’s Cancer Issue this month, for example, I read about a group that’s using the PGM for a clinical test comprising 100 common mutations in human cancers.

Essentially, the niche for PGM, MiSeq, and GS Junior is everything that’s not quite enough for a full-on sequencing run. A few examples come to mind:

1. Microbial sequencing. For bite-sized genomes, 1 Gbp should be more than enough. Imagine walking into a clinic to have your strain of Streptococcus or some other infection sequenced the same day.
2. Family linkage studies. With a few family members and a reasonably-sized linkage peak, you could sequence all gene-coding exons across a region of interest, either by PCR or custom capture.
3. Orthogonal validation. Whole-genome and whole-exome studies might identify hundreds of putative mutations. Emphasis on putative. No matter how good your algorithms and filters are, there will be some false positives. Here’s an opportunity for a small, fast validation instrument. Preferably, you choose a different sequencing technology for validation (e.g. PGM for Illumina, MiSeq for SOLiD).

There are countless other potential applications; undoubtedly, investigators already have a few in mind. Access to high-throughput sequencing is getting less and less expensive. Now, you can have your own setup, for less than the price of a luxury sedan.

For more, see Keith Robison’s post at Omics! Omics! or Matthew Herber’s blog on Forbes.com.