The Ion Torrent PGM
A new approach to massively parallel sequencing
The newest entry on the Next-Generation sequencing scene is the Ion Torrent Personal Genome Machine (PGM) from Life Technologies that is now installed in the Laboratory of Molecular Technology (LMT). The PGM is a small bench top instrument that detects the release of H+ ions during the hydrolysis of the triphosphate moiety as nucleotides are incorporated into DNA using a semiconductor chip and hydrogen ion sensor.
The “314” microchip has a detector composed of more than 1.2 million miniaturized electrodes. The “316” microchip has a detector composed of ~6 million electrodes. The growth potential for this platform is significant as the major developments will come with modifications of the software and the microchips. Life Technologies has also released the “318” chip that contains ~11 million wells.
The Ion Torrent has increased in throughput with commensurate reductions in cost to provide many new opportunities for scientific inquiry. Amplicon sequencing of multiple genes in cancer pathways, capture of genomic regions, whole exome sequencing, RNA transcriptome, microbiome studies and whole genome sequencing can be facilitated by the introduction of the Ion Torrent technology.
The oblong design of the microchip contains millions of wells occupied by beads containing amplified copies of a single DNA strand. The image shows the distribution of bead loading in a 314 chip from an experiment at the LMT. The PGM uses an emulsion PCR based amplification of single molecules of DNA similar to the Roche 454 instrument and provides approximately 100,000 individual sequences of up to 200 bp at around 99% accuracy in a three hour sequencing run. There is an expectation that the sequencing length will improve over the next 1-2 years and will be comparable to the average read length that is achievable on the 454 platform. With dramatic increases in well density the PGM will likely achieve approximately 1 billion base pairs of high quality sequence in a three hour run within the next two years.
The LMT also has the OneTouch ® and its ES® module. This adjunct system to the PGM produces the emPCR, collects and enriches the prep fir DNA positive ISPs. This effectively doubles the output of a single staff member.We are testing several custom targeted library preparation and sequencing protocols for the PGM. The team has performed over 200 sequencing runs to test improvements in the library creation and sample processing protocols.