Tool kit: Ion Personal Genome Machine

By Eleni Kanavas

The Ion Personal Genome Machine(PGM) by Life Technologies is the only known next-generation DNA sequencing system to use natural biochemistry instead of expensive laser optics to translate chemical information into digital data. The sequencer, with Ion AmpliSeq technology and a Torrent Server, performs real-time measurements of hydrogen ions released during nucleotide addition. It can deliver fast results with accurate targeted gene sequencing of specific genes or genomic regions in cancer and genetic disorders in less than three hours.

Dr. Arun Seth, a senior scientistin Biological Sciences, and head of the genomics facility at Sunnybrook Research Institute (SRI) is using the system in collaboration with clinician-scientists at SRI to study cancers of the head and neck, breast, thyroid and pancreas. He is also working with researchers in Saudi Arabia to compare breast cancer populations in Canada and Saudi Arabia. They are looking at the similarities and differences in breast cancer mutations.

The small bench-top system also produces accurate long reads with a raw read accuracy of more than 99% for 200-base sequencing, and maintains a high level of accuracy up to 400 bases. It has the lowest observed substitution error rate of any available next-generation sequencer.

Genomics facility manager Dr. Yutaka Amemiya can analyze up to 96 samples with available kits, or as many as 384 samples using custom barcodes, demonstrating the system’s flexibility. The Ion PGM sequencer is also more scalable than any other sequencing technology and supports a range of outputs with three ion semiconductor chips providing flexibility for projects.

Sunnybrook Research Institute installed the Ion PGM sequencing system in May 2013. It is worth $100,000 and was funded by the Canada Foundation for Innovation.