Thermo Fisher Scientific’s Ion S5 systems for targeted sequencing
The Ion S5 and Ion S5 XL benchtop systems use Ion Torrent technology and can be scaled for research areas, including infectious agents and microbial identification.
The systems combine the ability to sequence gene panels and small genomes, as well as exomes, transcriptomes and custom assays on one platform.
They are designed with ‘plug-and-play,’ cartridge-based reagents to help with setting up and operating the sequencers.
NGS in outbreak investigation and other applications
Andy Felton, VP of product management at Thermo Fisher Scientific, said primarily NGS is used in outbreak situations but it has potential in quality testing and microbiology control.
“For example, in the E.coli outbreak in 2011 it was used to sequence strains of the E.coli genome to find out where it came from and traceback in the supply chain,” he told FoodQualityNews.
“There are examples of that in foodborne outbreaks in the USA and Europe. Speed matters to see how different the strain is from what we have seen before.
“Beyond that applications include adulteration like the horse meat issue. NGS tells you what is in the sample, what organisms are in the product so for purity, adulteration or contamination concerns and checking for something that is not supposed to be there.
“It is used in species identification such as fish. What organism it is with one fish being passed off as a different one because it is more expensive or a protected species – is it what the label says. Another use is genotyping of populations such as salmon to see where is the catch coming from.”
The systems require 15 minutes of manual set-up time per sequencing run and less than 45 minutes of hands-on work from DNA to data when using the Ion Chef System for automated Ion AmpliSeq library construction, template preparation and chip loading.
The Ion S5 system is for academic or translational labs in need of an all-in-one sequencer without turnaround time constraints, while the Ion S5 XL system is for clinical research labs requiring faster turnaround or higher sample throughput per day.
It features three new Ion chips; the Ion 520, 530 and 540, which offer outputs of 5m to 80m sequencing reads generated in 2.5 hours.
The Ion Chef System provides automated, high-throughput template preparation and reproducible chip loading for users.
NGS industry foothold
Felton said NGS systems are in the phase of early adopters but old-line technology is still present.
“Big conglomerates are adopting it to drive how cost efficient they can be, for example, if you are genotyping 10,000 cattle it is a matter of cost but in foodborne outbreaks it is more around time and seeing if existing technology can do it as quick.
“It is the third generation – in 2010 was Ion PGM and in 2012 was the ION proton – the primary thing that has been developed is the ease of use.
“On the original PGM it was a mostly manual workflow process, now with ‘plug-and-play,’ cartridge-based reagents pre-filled and ready to use it is automated and you can tackle projects on different scales and with different chips.
“The decision on which system depends on time to result and throughput you need. With the Ion S5 you can do a run in two hours but data analysis takes about 5-20 hours and on S5 XL analysis takes one to five hours, so it is how quickly you need the result and how often you run the system.”
Labs need a kits and device for extraction of nucleic acid from the sample but little else in terms of infrastructure, said the firm.
Chris Linthwaite, president of Genetic Sciences at Thermo Fisher Scientific, said the Ion S5 system has many advantages offered by targeted sequencing.
“The genomics information revolution of the past decade has ushered in an exciting new era for a broad range of industries seeking to tackle fundamental problems of health, safety and security.
“We have developed the next generation of benchtop sequencing that delivers best-in-class workflow simplicity, integrated data analysis and system economics.”